def get_component():
component = hierachical_iaf_2coba.get_component()
comp = flattening.flatten(component)
# Remap some ports:
RenameSymbol(comp, 'iaf_vthresh', 'V_th')
RenameSymbol(comp, 'iaf_vreset', 'V_reset')
RenameSymbol(comp, 'iaf_taurefrac', 't_ref')
RenameSymbol(comp, 'iaf_vrest', 'E_L')
RenameSymbol(comp, 'iaf_cm', 'C_m')
RenameSymbol(comp, 'iaf_gl', 'g_L')
RenameSymbol(comp, 'cobaExcit_vrev', 'E_ex')
RenameSymbol(comp, 'cobaInhib_vrev', 'E_in')
RenameSymbol(comp, 'cobaInhib_q', 'q_in')
RenameSymbol(comp, 'cobaExcit_q', 'q_ex')
RenameSymbol(comp, 'cobaExcit_tau', 'tau_syn_ex')
RenameSymbol(comp, 'cobaInhib_tau', 'tau_syn_in')
RenameSymbol(comp, 'iaf_V', 'V_m')
RenameSymbol(comp, 'iaf_tspike', 'tspike')
RenameSymbol(comp, 'cobaInhib_g', 'g_in')
RenameSymbol(comp, 'cobaExcit_g', 'g_ex')
RenameSymbol(comp, 'cobaInhib_spikeinput', 'spike_in')
RenameSymbol(comp, 'cobaExcit_spikeinput', 'spike_ex')
return comp
def test(cls, testable_component, build_dir):
component = testable_component()
print " -- Testing One and a half trips..."
if not component.is_flat():
component = flattening.flatten(component)
xmlfile1 = build_dir + component.name + "1.xml"
xmlfile2 = build_dir + component.name + "2.xml"
print " -- Saving Component To XML:", xmlfile1
writers.XMLWriter.write(component, xmlfile1)
print " -- Loading Component To XML."
reloaded_comp = readers.XMLReader.read(xmlfile1)
print " -- Checking Components are identical"
validators.ComponentEqualityChecker.check_equal(component, reloaded_comp)
print " -- Saving Reloaded Component to XML", xmlfile2
writers.XMLWriter.write(reloaded_comp, xmlfile2)
print " -- Checking the SHA1 Checksum of the two xml files:"
hash1 = file_sha1_hexdigest(xmlfile1)
hash2 = file_sha1_hexdigest(xmlfile2)
print " -->", hash1
print " -->", hash2
if hash1 != hash2:
raise ValueError("XML files are different. This may not be an error but please report it to the developers")
def test_Flattening1(self):
c = ComponentClass(
name='C',
aliases=['C1:=cp1', 'C2 := cIn1', 'C3 := SV1'],
regimes=[
Regime(
'dSV1/dt = -SV1/cp2',
transitions=[On('SV1>cp1', do=[OutputEvent('emit')]),
On('spikein', do=[OutputEvent('c_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']
)
d = ComponentClass(
name='D',
aliases=['D1:=dp1', 'D2 := dIn1', 'D3 := SV1'],
regimes=[
Regime(
'dSV1/dt = -SV1/dp2',
transitions=[On('SV1>dp1', do=[OutputEvent('emit')]),
On('spikein', do=[OutputEvent('d_emit')])],
name='r1',
),
Regime(name='r2', transitions=On('SV1>1', to='r1'))
],
analog_ports=[RecvPort('dIn1'), RecvPort('dIn2'), SendPort('D1'), SendPort('D2')],
parameters=['dp1', 'dp2']
)
# Flatten a flat component
# Everything should be as before:
c_flat = flattening.flatten(c)
assert c_flat is not c
self.assertEqual(c_flat.name, 'C')
self.assertEqual(set(c_flat.aliases_map.keys()), set(['C1', 'C2', 'C3']))
# - Regimes and Transitions:
self.assertEqual(set(c_flat.regimes_map.keys()), set(['r1', 'r2']))
self.assertEqual(len(list(c_flat.regimes_map['r1'].on_events)), 1)
self.assertEqual(len(list(c_flat.regimes_map['r1'].on_conditions)), 1)
self.assertEqual(len(list(c_flat.regimes_map['r2'].on_events)), 0)
self.assertEqual(len(list(c_flat.regimes_map['r2'].on_conditions)), 1)
self.assertEqual(len(list(c_flat.regimes_map['r2'].on_conditions)), 1)
# - Ports & Parameters:
self.assertEqual(
set(c_flat.query.analog_ports_map.keys()), set(['cIn2', 'cIn1', 'C1', 'C2']))
self.assertEqual(
set(c_flat.query.event_ports_map.keys()), set(['spikein', 'c_emit', 'emit']))
self.assertEqual(set(c_flat.query.parameters_map.keys()), set(['cp1', 'cp2']))
self.assertEqual(set(c_flat.state_variables_map.keys()), set(['SV1']))
def write_and_compile_nmodl(component):
build_dir = os.path.join(BUILD_DIR, component.name.replace('-', '_'))
clear_and_recreate_dir(build_dir)
if not component.is_flat():
component = flatten(component)
ComponentModifier.close_all_reduce_ports(component=component)
print ' -- Writing Component to .mod'
modfilename = os.path.join(build_dir, component.name + '.mod').replace('-', '_')
write_nmodldirect(component=component, mod_filename=modfilename, weight_variables={})
compile_nmodl(build_dir)
def __new__(cls, name, bases, dct):
import nineml.abstraction_layer as al
from nineml.abstraction_layer import flattening, writers, component_modifiers
#Extract Parameters Back out from Dict:
combined_model = dct['nineml_model']
synapse_components = dct['synapse_components']
# Flatten the model:
assert isinstance(combined_model, al.ComponentClass)
if combined_model.is_flat():
flat_component = combined_model
else:
flat_component = flattening.flatten( combined_model,name )
# Make the substitutions:
flat_component.backsub_all()
#flat_component.backsub_aliases()
#flat_component.backsub_equations()
# Close any open reduce ports:
component_modifiers.ComponentModifier.close_all_reduce_ports(component = flat_component)
# New:
dct["combined_model"] = flat_component
dct["default_parameters"] = dict( (param.name, 1.0) for param in flat_component.parameters )
dct["default_initial_values"] = dict((statevar.name, 0.0) for statevar in chain(flat_component.state_variables) )
dct["synapse_types"] = [syn.namespace for syn in synapse_components]
dct["standard_receptor_type"] = (dct["synapse_types"] == ('excitatory', 'inhibitory'))
dct["injectable"] = True # need to determine this. How??
dct["conductance_based"] = True # how to determine this??
dct["model_name"] = name
# Recording from bindings:
dct["recordable"] = [port.name for port in flat_component.analog_ports] + ['spikes', 'regime'] + [alias.lhs for alias in flat_component.aliases] + [statevar.name for statevar in flat_component.state_variables]
dct["weight_variables"] = dict([ (syn.namespace,syn.namespace+'_'+syn.weight_connector )
for syn in synapse_components ])
logger.debug("Creating class '%s' with bases %s and dictionary %s" % (name, bases, dct))
# generate and compile NMODL code, then load the mechanism into NEUORN
dct["builder"](flat_component, dct["weight_variables"], hierarchical_mode=True)
return type.__new__(cls, name, bases, dct)
def func_test(self):
emitter = ComponentClass(
name="EventEmitter",
parameters=["cyclelength"],
regimes=[Regime(transitions=On("t > tchange + cyclelength", do=[OutputEvent("emit"), "tchange=t"]))],
)
ev_based_cc = ComponentClass(
name="EventBasedCurrentClass",
parameters=["dur", "i"],
analog_ports=[SendPort("I")],
regimes=[
Regime(
transitions=[
On("inputevent", do=["I=i", "tchange = t"]),
On("t>tchange + dur", do=["I=0", "tchange=t"]),
]
)
],
)
pulsing_emitter = ComponentClass(
name="pulsing_cc",
subnodes={"evs": emitter, "cc": ev_based_cc},
portconnections=[("evs.emit", "cc.inputevent")],
)
nrn = ComponentClass(
name="LeakyNeuron",
parameters=["Cm", "gL", "E"],
regimes=[Regime("dV/dt = (iInj + (E-V)*gL )/Cm")],
aliases=["iIn := iInj"],
analog_ports=[SendPort("V"), ReducePort("iInj", reduce_op="+")],
)
combined_comp = ComponentClass(
name="Comp1",
subnodes={"nrn": nrn, "cc1": pulsing_emitter, "cc2": pulsing_emitter},
portconnections=[("cc1.cc.I", "nrn.iInj"), ("cc2.cc.I", "nrn.iInj")],
)
combined_comp = 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 = 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,
}
)
res = std_pynn_simulation(
test_component=combined_comp,
parameters=parameters,
initial_values={},
synapse_components=[],
records=records,
# plot = False,
)
return
t, records = res
def check_trace(trace_name, time_period, exp_mean, exp_std=0):
t_indices = (t > time_period[0] + 1) & (t < time_period[1] - 1)
self.assertAlmostEqual(records[trace_name][t_indices].mean(), exp_mean, places=3)
self.assertAlmostEqual(records[trace_name][t_indices].std(), exp_std, places=3)
check_trace("cc1_cc_I", (00, 30), exp_mean=0.0)
check_trace("cc1_cc_I", (30, 40), exp_mean=13.8)
check_trace("cc1_cc_I", (40, 60), exp_mean=0.0)
check_trace("cc1_cc_I", (60, 70), exp_mean=13.8)
check_trace("cc1_cc_I", (70, 90), exp_mean=0.0)
check_trace("cc1_cc_I", (90, 100), exp_mean=13.8)
check_trace("cc2_cc_I", (00, 20), exp_mean=0.0)
check_trace("cc2_cc_I", (20, 25), exp_mean=20.8)
check_trace("cc2_cc_I", (25, 40), exp_mean=0.0)
check_trace("cc2_cc_I", (40, 45), exp_mean=20.8)
check_trace("cc2_cc_I", (45, 60), exp_mean=0.0)
check_trace("cc2_cc_I", (60, 65), exp_mean=20.8)
check_trace("cc2_cc_I", (65, 80), exp_mean=0.0)
check_trace("cc2_cc_I", (80, 85), exp_mean=20.8)
check_trace("cc2_cc_I", (85, 100), exp_mean=0.0)
check_trace("nrn_iIn", (00, 20), exp_mean=0.0)
check_trace("nrn_iIn", (20, 25), exp_mean=20.8)
check_trace("nrn_iIn", (25, 30), exp_mean=0.0)
check_trace("nrn_iIn", (30, 40), exp_mean=13.8)
check_trace("nrn_iIn", (40, 45), exp_mean=20.8)
check_trace("nrn_iIn", (45, 60), exp_mean=0.0)
check_trace("nrn_iIn", (60, 65), exp_mean=34.6)
check_trace("nrn_iIn", (65, 70), exp_mean=13.8)
check_trace("nrn_iIn", (70, 80), exp_mean=0.0)
check_trace("nrn_iIn", (80, 85), exp_mean=20.8)
check_trace("nrn_iIn", (85, 90), exp_mean=0.0)
check_trace("nrn_iIn", (90, 100), exp_mean=13.8)
check_trace("nrn_V", (00 + 2, 20), exp_mean=(0.0 / 4.3) - 70)
check_trace("nrn_V", (20 + 2, 25), exp_mean=(20.8 / 4.3) - 70)
check_trace("nrn_V", (25 + 2, 30), exp_mean=(0.0 / 4.3) - 70)
check_trace("nrn_V", (30 + 2, 40), exp_mean=(13.8 / 4.3) - 70)
check_trace("nrn_V", (40 + 2, 45), exp_mean=(20.8 / 4.3) - 70)
check_trace("nrn_V", (45 + 2, 60), exp_mean=(0.0 / 4.3) - 70)
check_trace("nrn_V", (60 + 2, 65), exp_mean=(34.6 / 4.3) - 70)
check_trace("nrn_V", (65 + 2, 70), exp_mean=(13.8 / 4.3) - 70)
check_trace("nrn_V", (70 + 2, 80), exp_mean=(0.0 / 4.3) - 70)
check_trace("nrn_V", (80 + 2, 85), exp_mean=(20.8 / 4.3) - 70)
check_trace("nrn_V", (85 + 2, 90), exp_mean=(0.0 / 4.3) - 70)
check_trace("nrn_V", (90 + 2, 100), exp_mean=(13.8 / 4.3) - 70)
def func_test(self):
emitter = ComponentClass(
name='EventEmitter',
parameters=['cyclelength'],
regimes=[
Regime(transitions=On('t > tchange + random_offset + cyclelength',
do=[OutputEvent(
'emit'), 'tchange=t', 'random_offset=random.uniform(5,10) '])),
])
ev_based_cc = ComponentClass(
name='EventBasedCurrentClass',
parameters=['dur', 'i'],
analog_ports=[SendPort('I')],
regimes=[
Regime(
transitions=[
On('inputevent', do=['I=i', 'tchange = t', ]),
On('t>tchange + dur ', do=['I=0', 'tchange=t'])
]
)
]
)
pulsing_emitter = ComponentClass(name='pulsing_cc',
subnodes={'evs': emitter, 'cc': ev_based_cc},
portconnections=[('evs.emit', 'cc.inputevent')]
)
nrn = ComponentClass(
name='LeakyNeuron',
parameters=['Cm', 'gL', 'E'],
regimes=[Regime('dV/dt = (iInj + (E-V)*gL )/Cm'), ],
aliases=['iIn := iInj'],
analog_ports=[SendPort('V'),
ReducePort('iInj', reduce_op='+')],
)
combined_comp = ComponentClass(name='Comp1',
subnodes={'nrn': nrn,
'cc1': pulsing_emitter,
'cc2': pulsing_emitter},
portconnections=[('cc1.cc.I', 'nrn.iInj'),
('cc2.cc.I', 'nrn.iInj')]
)
combined_comp = 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 = flattening.ComponentFlattener.flatten_namespace_dict({
'cc1.cc.i': 13.8,
'cc1.cc.dur': 5,
'cc1.evs.cyclelength': 15,
'cc2.cc.i': 20.8,
'cc2.cc.dur': 5,
'cc2.evs.cyclelength': 15,
'nrn.gL': 4.3,
'nrn.E': -70})
res = std_pynn_simulation(test_component=combined_comp,
parameters=parameters,
initial_values={},
synapse_components=[],
records=records,
# plot = False,
)
return
t, records = res
def check_trace(trace_name, time_period, exp_mean, exp_std=0):
t_indices = (t > time_period[0] + 1) & (t < time_period[1] - 1)
self.assertAlmostEqual(records[trace_name][t_indices].mean(), exp_mean, places=3)
self.assertAlmostEqual(records[trace_name][t_indices].std(), exp_std, places=3)
#import os
from nineml.abstraction_layer.testing_utils import TestableComponent
from nineml.abstraction_layer.flattening import flatten
#from nineml.abstraction_layer.flattening import ComponentFlattener
from nineml.abstraction_layer.component_modifiers import ComponentModifier
from nineml.utility import LocationMgr
#from nineml.abstraction_layer.visitors import RenameSymbol
LocationMgr.StdAppendToPath()
comp_data = TestableComponent('nestequivalent_iaf_cond_exp')
# Build the component:
component = comp_data()
component = flatten( component )
component.backsub_all()
ComponentModifier.close_all_reduce_ports(component=component)
# Copy the descriptive strings:
component.short_description = comp_data.metadata.short_description
component.long_description = comp_data.metadata.long_description
# Get the initial regime. If this component comes from an flattened component,
# then we should look up the new regime from the locations in the old
# components, hence the nedd for this code:
initial_regime = comp_data.metadata.initial_regime
if component.was_flattened():
def test_Flattening2(self):
c = ComponentClass(
name='C',
aliases=['C1:=cp1', 'C2 := cIn1', 'C3 := SV1'],
regimes=[
Regime(
'dSV1/dt = -SV1/cp2',
transitions=[On('SV1>cp1', do=[OutputEvent('emit')]),
On('spikein', do=[OutputEvent('c_emit')])],
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 = ComponentClass(
name='D',
aliases=['D1:=dp1', 'D2 := dIn1', 'D3 := SV1'],
regimes=[
Regime(
'dSV1/dt = -SV1/dp2',
transitions=[On('SV1>dp1', do=[OutputEvent('emit')]),
On('spikein', do=[OutputEvent('d_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']
)
# Test Cloner, 1 level of hierachy
# ------------------------------ #
# Everything should be as before:
b = ComponentClass(name='B',
subnodes={'c1': c, 'c2': c, 'd': d},
# portconnections= [('c1.C1','c2.cIn1'),('c2.emit','c1.spikein'), ]
)
b_flat = flattening.flatten(b)
# Name
self.assertEqual(b_flat.name, 'B')
# Aliases
self.assertEqual(
set(b_flat.aliases_map.keys()),
set(['c1_C1', 'c1_C2', 'c1_C3', 'c2_C1', 'c2_C2', 'c2_C3', 'd_D1', 'd_D2', 'd_D3']))
# - Regimes and Transitions:
self.assertEqual(len(b_flat.regimes_map), 8)
r_c1_1_c2_1_d_1 = b_flat.flattener.get_new_regime('d:r1 c1:r1 c2:r1 ')
r_c1_1_c2_2_d_1 = b_flat.flattener.get_new_regime('d:r1 c1:r1 c2:r2 ')
r_c1_2_c2_1_d_1 = b_flat.flattener.get_new_regime('d:r1 c1:r2 c2:r1')
r_c1_2_c2_2_d_1 = b_flat.flattener.get_new_regime('d:r1 c1:r2 c2:r2')
r_c1_1_c2_1_d_2 = b_flat.flattener.get_new_regime('d:r2 c1:r1 c2:r1 ')
r_c1_1_c2_2_d_2 = b_flat.flattener.get_new_regime('d:r2 c1:r1 c2:r2 ')
r_c1_2_c2_1_d_2 = b_flat.flattener.get_new_regime('d:r2 c1:r2 c2:r1')
r_c1_2_c2_2_d_2 = b_flat.flattener.get_new_regime('d:r2 c1:r2 c2:r2')
# Do we have the right number of on_events and on_conditions:
self.assertEqual(len(list(r_c1_1_c2_1_d_1.on_events)), 3)
self.assertEqual(len(list(r_c1_1_c2_1_d_1.on_conditions)), 3)
self.assertEqual(len(list(r_c1_1_c2_2_d_1.on_events)), 2)
self.assertEqual(len(list(r_c1_1_c2_2_d_1.on_conditions)), 3)
self.assertEqual(len(list(r_c1_2_c2_1_d_1.on_events)), 2)
self.assertEqual(len(list(r_c1_2_c2_1_d_1.on_conditions)), 3)
self.assertEqual(len(list(r_c1_2_c2_2_d_1.on_events)), 1)
self.assertEqual(len(list(r_c1_2_c2_2_d_1.on_conditions)), 3)
self.assertEqual(len(list(r_c1_1_c2_1_d_2.on_events)), 2)
self.assertEqual(len(list(r_c1_1_c2_1_d_2.on_conditions)), 3)
self.assertEqual(len(list(r_c1_1_c2_2_d_2.on_events)), 1)
self.assertEqual(len(list(r_c1_1_c2_2_d_2.on_conditions)), 3)
self.assertEqual(len(list(r_c1_2_c2_1_d_2.on_events)), 1)
self.assertEqual(len(list(r_c1_2_c2_1_d_2.on_conditions)), 3)
self.assertEqual(len(list(r_c1_2_c2_2_d_2.on_events)), 0)
self.assertEqual(len(list(r_c1_2_c2_2_d_2.on_conditions)), 3)
# All on_events return to thier same transition:
self.assertEqual((list(r_c1_1_c2_1_d_1.on_events))[0].target_regime, r_c1_1_c2_1_d_1)
self.assertEqual((list(r_c1_1_c2_1_d_1.on_events))[1].target_regime, r_c1_1_c2_1_d_1)
self.assertEqual((list(r_c1_1_c2_1_d_1.on_events))[2].target_regime, r_c1_1_c2_1_d_1)
self.assertEqual((list(r_c1_1_c2_2_d_1.on_events))[0].target_regime, r_c1_1_c2_2_d_1)
self.assertEqual((list(r_c1_1_c2_2_d_1.on_events))[1].target_regime, r_c1_1_c2_2_d_1)
self.assertEqual((list(r_c1_2_c2_1_d_1.on_events))[0].target_regime, r_c1_2_c2_1_d_1)
self.assertEqual((list(r_c1_2_c2_1_d_1.on_events))[1].target_regime, r_c1_2_c2_1_d_1)
self.assertEqual((list(r_c1_2_c2_2_d_1.on_events))[0].target_regime, r_c1_2_c2_2_d_1)
self.assertEqual((list(r_c1_1_c2_1_d_2.on_events))[0].target_regime, r_c1_1_c2_1_d_2)
self.assertEqual((list(r_c1_1_c2_1_d_2.on_events))[1].target_regime, r_c1_1_c2_1_d_2)
self.assertEqual((list(r_c1_1_c2_2_d_2.on_events))[0].target_regime, r_c1_1_c2_2_d_2)
self.assertEqual((list(r_c1_2_c2_1_d_2.on_events))[0].target_regime, r_c1_2_c2_1_d_2)
# Check On-Event port names are remapped properly:
self.assertEqual(set([ev.src_port_name for ev in r_c1_1_c2_1_d_1.on_events]), set(
['c1_spikein', 'c2_spikein', 'd_spikein']))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_1_c2_2_d_1.on_events]), set(['c1_spikein', 'd_spikein']))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_2_c2_1_d_1.on_events]), set(['c2_spikein', 'd_spikein']))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_2_c2_2_d_1.on_events]), set(['d_spikein']))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_1_c2_1_d_2.on_events]), set(['c1_spikein', 'c2_spikein']))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_1_c2_2_d_2.on_events]), set(['c1_spikein', ]))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_2_c2_1_d_2.on_events]), set(['c2_spikein', ]))
self.assertEqual(set([ev.src_port_name for ev in r_c1_2_c2_2_d_2.on_events]), set([]))
# ToDo: Check the OnConditions:
# - Ports & Parameters:
self.assertEqual(
set(b_flat.query.analog_ports_map.keys()),
set(['c1_cIn1', 'c1_cIn2', 'c1_C1', 'c1_C2', 'c2_cIn1', 'c2_cIn2', 'c2_C1', 'c2_C2', 'd_dIn1', 'd_dIn2', 'd_D1', 'd_D2']))
self.assertEqual(
set(b_flat.query.event_ports_map.keys()),
set(['c1_spikein', 'c1_emit', 'c1_c_emit', 'c2_spikein', 'c2_emit', 'c2_c_emit', 'd_spikein', 'd_emit', 'd_d_emit']))
self.assertEqual(
set(b_flat.query.parameters_map.keys()),
set(['c1_cp1', 'c1_cp2', 'c2_cp1', 'c2_cp2', 'd_dp1', 'd_dp2', ]))
self.assertEqual(
set(b_flat.state_variables_map.keys()),
set(['c1_SV1', 'c2_SV1', 'd_SV1']))
def func_test(self):
emitter = ComponentClass(
name='EventEmitter',
parameters=['rate'],
regimes=[
Regime(
transitions=On(
't > tchange', do=[OutputEvent('emit'), 'tchange=t + random.exponential(1/rate) '])),
])
ev_based_cc = ComponentClass(
name='EventBasedCurrentClass',
parameters=['dur', 'i'],
analog_ports=[SendPort('I')],
regimes=[
Regime(
transitions=[
On('inputevent', do=['I=i', 'tchange = t']),
On('t>tchange + dur', do=['I=0', 'tchange=t'])
]
)
]
)
pulsing_emitter = ComponentClass(name='pulsing_cc',
subnodes={'evs': emitter, 'cc': ev_based_cc},
portconnections=[('evs.emit', 'cc.inputevent')]
)
nrn = ComponentClass(
name='LeakyNeuron',
parameters=['Cm', 'gL', 'E'],
regimes=[Regime('dV/dt = (iInj + (E-V)*gL )/Cm'), ],
aliases=['iIn := iInj'],
analog_ports=[SendPort('V'),
ReducePort('iInj', reduce_op='+')],
)
combined_comp = ComponentClass(name='Comp1',
subnodes={
'nrn': nrn, 'cc1': pulsing_emitter, 'cc2': pulsing_emitter},
portconnections=[('cc1.cc.I', 'nrn.iInj'),
('cc2.cc.I', 'nrn.iInj')]
)
combined_comp = 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 = flattening.ComponentFlattener.flatten_namespace_dict({
'cc1.cc.i': 13.8,
'cc1.cc.dur': 1,
'cc1.evs.rate': 110. / 1000.,
'cc2.cc.i': 20.8,
'cc2.cc.dur': 1.,
'cc2.evs.rate': 20. / 1000.,
'nrn.gL': 4.3,
'nrn.E': -70})
res = std_pynn_simulation(test_component=combined_comp,
parameters=parameters,
initial_values={},
synapse_components=[],
records=records,
sim_time=1000
# plot = False,
)
return
t, records = res
def check_trace(trace_name, time_period, exp_mean, exp_std=0):
t_indices = (t > time_period[0] + 1) & (t < time_period[1] - 1)
self.assertAlmostEqual(records[trace_name][t_indices].mean(), exp_mean, places=3)
self.assertAlmostEqual(records[trace_name][t_indices].std(), exp_std, places=3)
check_trace('cc1_cc_I', (00, 30), exp_mean=0.0)
check_trace('cc1_cc_I', (30, 40), exp_mean=13.8)
check_trace('cc1_cc_I', (40, 60), exp_mean=0.0)
check_trace('cc1_cc_I', (60, 70), exp_mean=13.8)
check_trace('cc1_cc_I', (70, 90), exp_mean=0.0)
check_trace('cc1_cc_I', (90, 100), exp_mean=13.8)
check_trace('cc2_cc_I', (00, 20), exp_mean=0.0)
check_trace('cc2_cc_I', (20, 25), exp_mean=20.8)
check_trace('cc2_cc_I', (25, 40), exp_mean=0.0)
check_trace('cc2_cc_I', (40, 45), exp_mean=20.8)
check_trace('cc2_cc_I', (45, 60), exp_mean=0.0)
check_trace('cc2_cc_I', (60, 65), exp_mean=20.8)
check_trace('cc2_cc_I', (65, 80), exp_mean=0.0)
check_trace('cc2_cc_I', (80, 85), exp_mean=20.8)
check_trace('cc2_cc_I', (85, 100), exp_mean=0.0)
check_trace('nrn_iIn', (00, 20), exp_mean=0.0)
check_trace('nrn_iIn', (20, 25), exp_mean=20.8)
check_trace('nrn_iIn', (25, 30), exp_mean=0.0)
check_trace('nrn_iIn', (30, 40), exp_mean=13.8)
check_trace('nrn_iIn', (40, 45), exp_mean=20.8)
check_trace('nrn_iIn', (45, 60), exp_mean=0.0)
check_trace('nrn_iIn', (60, 65), exp_mean=34.6)
check_trace('nrn_iIn', (65, 70), exp_mean=13.8)
check_trace('nrn_iIn', (70, 80), exp_mean=0.0)
check_trace('nrn_iIn', (80, 85), exp_mean=20.8)
check_trace('nrn_iIn', (85, 90), exp_mean=0.0)
check_trace('nrn_iIn', (90, 100), exp_mean=13.8)
check_trace('nrn_V', (00 + 2, 20), exp_mean=(0.0 / 4.3) - 70)
check_trace('nrn_V', (20 + 2, 25), exp_mean=(20.8 / 4.3) - 70)
check_trace('nrn_V', (25 + 2, 30), exp_mean=(0.0 / 4.3) - 70)
check_trace('nrn_V', (30 + 2, 40), exp_mean=(13.8 / 4.3) - 70)
check_trace('nrn_V', (40 + 2, 45), exp_mean=(20.8 / 4.3) - 70)
check_trace('nrn_V', (45 + 2, 60), exp_mean=(0.0 / 4.3) - 70)
check_trace('nrn_V', (60 + 2, 65), exp_mean=(34.6 / 4.3) - 70)
check_trace('nrn_V', (65 + 2, 70), exp_mean=(13.8 / 4.3) - 70)
check_trace('nrn_V', (70 + 2, 80), exp_mean=(0.0 / 4.3) - 70)
check_trace('nrn_V', (80 + 2, 85), exp_mean=(20.8 / 4.3) - 70)
check_trace('nrn_V', (85 + 2, 90), exp_mean=(0.0 / 4.3) - 70)
check_trace('nrn_V', (90 + 2, 100), exp_mean=(13.8 / 4.3) - 70)
def test_Flattening2(self):
c = ComponentClass(name='C',
aliases=['C1:=cp1', 'C2 := cIn1', 'C3 := SV1'],
regimes=[
Regime(
'dSV1/dt = -SV1/cp2',
transitions=[
On('SV1>cp1', do=[OutputEvent('emit')]),
On('spikein',
do=[OutputEvent('c_emit')])
],
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 = ComponentClass(name='D',
aliases=['D1:=dp1', 'D2 := dIn1', 'D3 := SV1'],
regimes=[
Regime(
'dSV1/dt = -SV1/dp2',
transitions=[
On('SV1>dp1', do=[OutputEvent('emit')]),
On('spikein',
do=[OutputEvent('d_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'])
# Test Cloner, 1 level of hierachy
# ------------------------------ #
# Everything should be as before:
b = ComponentClass(
name='B',
subnodes={
'c1': c,
'c2': c,
'd': d
},
# portconnections= [('c1.C1','c2.cIn1'),('c2.emit','c1.spikein'), ]
)
b_flat = flattening.flatten(b)
# Name
self.assertEqual(b_flat.name, 'B')
# Aliases
self.assertEqual(
set(b_flat.aliases_map.keys()),
set([
'c1_C1', 'c1_C2', 'c1_C3', 'c2_C1', 'c2_C2', 'c2_C3', 'd_D1',
'd_D2', 'd_D3'
]))
# - Regimes and Transitions:
self.assertEqual(len(b_flat.regimes_map), 8)
r_c1_1_c2_1_d_1 = b_flat.flattener.get_new_regime('d:r1 c1:r1 c2:r1 ')
r_c1_1_c2_2_d_1 = b_flat.flattener.get_new_regime('d:r1 c1:r1 c2:r2 ')
r_c1_2_c2_1_d_1 = b_flat.flattener.get_new_regime('d:r1 c1:r2 c2:r1')
r_c1_2_c2_2_d_1 = b_flat.flattener.get_new_regime('d:r1 c1:r2 c2:r2')
r_c1_1_c2_1_d_2 = b_flat.flattener.get_new_regime('d:r2 c1:r1 c2:r1 ')
r_c1_1_c2_2_d_2 = b_flat.flattener.get_new_regime('d:r2 c1:r1 c2:r2 ')
r_c1_2_c2_1_d_2 = b_flat.flattener.get_new_regime('d:r2 c1:r2 c2:r1')
r_c1_2_c2_2_d_2 = b_flat.flattener.get_new_regime('d:r2 c1:r2 c2:r2')
# Do we have the right number of on_events and on_conditions:
self.assertEqual(len(list(r_c1_1_c2_1_d_1.on_events)), 3)
self.assertEqual(len(list(r_c1_1_c2_1_d_1.on_conditions)), 3)
self.assertEqual(len(list(r_c1_1_c2_2_d_1.on_events)), 2)
self.assertEqual(len(list(r_c1_1_c2_2_d_1.on_conditions)), 3)
self.assertEqual(len(list(r_c1_2_c2_1_d_1.on_events)), 2)
self.assertEqual(len(list(r_c1_2_c2_1_d_1.on_conditions)), 3)
self.assertEqual(len(list(r_c1_2_c2_2_d_1.on_events)), 1)
self.assertEqual(len(list(r_c1_2_c2_2_d_1.on_conditions)), 3)
self.assertEqual(len(list(r_c1_1_c2_1_d_2.on_events)), 2)
self.assertEqual(len(list(r_c1_1_c2_1_d_2.on_conditions)), 3)
self.assertEqual(len(list(r_c1_1_c2_2_d_2.on_events)), 1)
self.assertEqual(len(list(r_c1_1_c2_2_d_2.on_conditions)), 3)
self.assertEqual(len(list(r_c1_2_c2_1_d_2.on_events)), 1)
self.assertEqual(len(list(r_c1_2_c2_1_d_2.on_conditions)), 3)
self.assertEqual(len(list(r_c1_2_c2_2_d_2.on_events)), 0)
self.assertEqual(len(list(r_c1_2_c2_2_d_2.on_conditions)), 3)
# All on_events return to thier same transition:
self.assertEqual((list(r_c1_1_c2_1_d_1.on_events))[0].target_regime,
r_c1_1_c2_1_d_1)
self.assertEqual((list(r_c1_1_c2_1_d_1.on_events))[1].target_regime,
r_c1_1_c2_1_d_1)
self.assertEqual((list(r_c1_1_c2_1_d_1.on_events))[2].target_regime,
r_c1_1_c2_1_d_1)
self.assertEqual((list(r_c1_1_c2_2_d_1.on_events))[0].target_regime,
r_c1_1_c2_2_d_1)
self.assertEqual((list(r_c1_1_c2_2_d_1.on_events))[1].target_regime,
r_c1_1_c2_2_d_1)
self.assertEqual((list(r_c1_2_c2_1_d_1.on_events))[0].target_regime,
r_c1_2_c2_1_d_1)
self.assertEqual((list(r_c1_2_c2_1_d_1.on_events))[1].target_regime,
r_c1_2_c2_1_d_1)
self.assertEqual((list(r_c1_2_c2_2_d_1.on_events))[0].target_regime,
r_c1_2_c2_2_d_1)
self.assertEqual((list(r_c1_1_c2_1_d_2.on_events))[0].target_regime,
r_c1_1_c2_1_d_2)
self.assertEqual((list(r_c1_1_c2_1_d_2.on_events))[1].target_regime,
r_c1_1_c2_1_d_2)
self.assertEqual((list(r_c1_1_c2_2_d_2.on_events))[0].target_regime,
r_c1_1_c2_2_d_2)
self.assertEqual((list(r_c1_2_c2_1_d_2.on_events))[0].target_regime,
r_c1_2_c2_1_d_2)
# Check On-Event port names are remapped properly:
self.assertEqual(
set([ev.src_port_name for ev in r_c1_1_c2_1_d_1.on_events]),
set(['c1_spikein', 'c2_spikein', 'd_spikein']))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_1_c2_2_d_1.on_events]),
set(['c1_spikein', 'd_spikein']))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_2_c2_1_d_1.on_events]),
set(['c2_spikein', 'd_spikein']))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_2_c2_2_d_1.on_events]),
set(['d_spikein']))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_1_c2_1_d_2.on_events]),
set(['c1_spikein', 'c2_spikein']))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_1_c2_2_d_2.on_events]),
set([
'c1_spikein',
]))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_2_c2_1_d_2.on_events]),
set([
'c2_spikein',
]))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_2_c2_2_d_2.on_events]),
set([]))
# ToDo: Check the OnConditions:
# - Ports & Parameters:
self.assertEqual(
set(b_flat.query.analog_ports_map.keys()),
set([
'c1_cIn1', 'c1_cIn2', 'c1_C1', 'c1_C2', 'c2_cIn1', 'c2_cIn2',
'c2_C1', 'c2_C2', 'd_dIn1', 'd_dIn2', 'd_D1', 'd_D2'
]))
self.assertEqual(
set(b_flat.query.event_ports_map.keys()),
set([
'c1_spikein', 'c1_emit', 'c1_c_emit', 'c2_spikein', 'c2_emit',
'c2_c_emit', 'd_spikein', 'd_emit', 'd_d_emit'
]))
self.assertEqual(
set(b_flat.query.parameters_map.keys()),
set([
'c1_cp1',
'c1_cp2',
'c2_cp1',
'c2_cp2',
'd_dp1',
'd_dp2',
]))
self.assertEqual(set(b_flat.state_variables_map.keys()),
set(['c1_SV1', 'c2_SV1', 'd_SV1']))
def test_Flattening1(self):
c = ComponentClass(name='C',
aliases=['C1:=cp1', 'C2 := cIn1', 'C3 := SV1'],
regimes=[
Regime(
'dSV1/dt = -SV1/cp2',
transitions=[
On('SV1>cp1', do=[OutputEvent('emit')]),
On('spikein',
do=[OutputEvent('c_emit')])
],
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 = ComponentClass(name='D',
aliases=['D1:=dp1', 'D2 := dIn1', 'D3 := SV1'],
regimes=[
Regime(
'dSV1/dt = -SV1/dp2',
transitions=[
On('SV1>dp1', do=[OutputEvent('emit')]),
On('spikein',
do=[OutputEvent('d_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'])
# Flatten a flat component
# Everything should be as before:
c_flat = flattening.flatten(c)
assert c_flat is not c
self.assertEqual(c_flat.name, 'C')
self.assertEqual(set(c_flat.aliases_map.keys()),
set(['C1', 'C2', 'C3']))
# - Regimes and Transitions:
self.assertEqual(set(c_flat.regimes_map.keys()), set(['r1', 'r2']))
self.assertEqual(len(list(c_flat.regimes_map['r1'].on_events)), 1)
self.assertEqual(len(list(c_flat.regimes_map['r1'].on_conditions)), 1)
self.assertEqual(len(list(c_flat.regimes_map['r2'].on_events)), 0)
self.assertEqual(len(list(c_flat.regimes_map['r2'].on_conditions)), 1)
self.assertEqual(len(list(c_flat.regimes_map['r2'].on_conditions)), 1)
# - Ports & Parameters:
self.assertEqual(set(c_flat.query.analog_ports_map.keys()),
set(['cIn2', 'cIn1', 'C1', 'C2']))
self.assertEqual(set(c_flat.query.event_ports_map.keys()),
set(['spikein', 'c_emit', 'emit']))
self.assertEqual(set(c_flat.query.parameters_map.keys()),
set(['cp1', 'cp2']))
self.assertEqual(set(c_flat.state_variables_map.keys()), set(['SV1']))
def test_Flattening4(self):
c = ComponentClass(
name='C',
aliases=['C1:=cp1', 'C2 := cIn1', 'C3 := SV1', 'C4:=cIn2'],
regimes=[
Regime(
'dSV1/dt = -SV1/cp2',
transitions=[
On('SV1>cp1', do=[OutputEvent('emit')]),
On('spikein', do=[OutputEvent('c_emit')])
],
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 = ComponentClass(
name='D',
aliases=['D1:=dp1', 'D2 := dIn1 + dp2', 'D3 := SV1'],
regimes=[
Regime(
'dSV1/dt = -SV1/dp2',
transitions=[
On('SV1>dp1', do=[OutputEvent('emit')]),
On('spikein', do=[OutputEvent('d_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'])
# Test Cloner, 2 levels of hierachy
# ------------------------------ #
# Everything should be as before:
b = ComponentClass(
name='B',
subnodes={
'c1': c,
'c2': c,
'd': d
},
portconnections=[('c1.C1', 'c2.cIn2'), ('c2.C1', 'c1.cIn1')],
)
a = ComponentClass(name='A',
subnodes={
'b': b,
'c': c
},
portconnections=[('b.c1.C1', 'b.c1.cIn2'),
('b.c1.C1', 'b.c2.cIn1'),
('b.c1.C2', 'b.d.dIn1')])
a_flat = flattening.flatten(a)
# Name
self.assertEqual(a_flat.name, 'A')
# Aliases
self.assertEqual(
set(a_flat.aliases_map.keys()),
set([
'b_c1_C1', 'b_c1_C2', 'b_c1_C3', 'b_c1_C4', 'b_c2_C1',
'b_c2_C2', 'b_c2_C3', 'b_c2_C4', 'b_d_D1', 'b_d_D2', 'b_d_D3',
'c_C1', 'c_C2', 'c_C3', 'c_C4'
]))
# - Regimes and Transitions:
self.assertEqual(len(a_flat.regimes_map), 16)
r_c1_1_c2_1_d_1_c_1 = a_flat.flattener.get_new_regime(
'b.d:r1 b.c1:r1 b.c2:r1 c:r1')
r_c1_1_c2_2_d_1_c_1 = a_flat.flattener.get_new_regime(
'b.d:r1 b.c1:r1 b.c2:r2 c:r1')
r_c1_2_c2_1_d_1_c_1 = a_flat.flattener.get_new_regime(
'b.d:r1 b.c1:r2 b.c2:r1 c:r1')
r_c1_2_c2_2_d_1_c_1 = a_flat.flattener.get_new_regime(
'b.d:r1 b.c1:r2 b.c2:r2 c:r1')
r_c1_1_c2_1_d_2_c_1 = a_flat.flattener.get_new_regime(
'b.d:r2 b.c1:r1 b.c2:r1 c:r1')
r_c1_1_c2_2_d_2_c_1 = a_flat.flattener.get_new_regime(
'b.d:r2 b.c1:r1 b.c2:r2 c:r1')
r_c1_2_c2_1_d_2_c_1 = a_flat.flattener.get_new_regime(
'b.d:r2 b.c1:r2 b.c2:r1 c:r1')
r_c1_2_c2_2_d_2_c_1 = a_flat.flattener.get_new_regime(
'b.d:r2 b.c1:r2 b.c2:r2 c:r1')
r_c1_1_c2_1_d_1_c_2 = a_flat.flattener.get_new_regime(
'b.d:r1 b.c1:r1 b.c2:r1 c:r2')
r_c1_1_c2_2_d_1_c_2 = a_flat.flattener.get_new_regime(
'b.d:r1 b.c1:r1 b.c2:r2 c:r2')
r_c1_2_c2_1_d_1_c_2 = a_flat.flattener.get_new_regime(
'b.d:r1 b.c1:r2 b.c2:r1 c:r2')
r_c1_2_c2_2_d_1_c_2 = a_flat.flattener.get_new_regime(
'b.d:r1 b.c1:r2 b.c2:r2 c:r2')
r_c1_1_c2_1_d_2_c_2 = a_flat.flattener.get_new_regime(
'b.d:r2 b.c1:r1 b.c2:r1 c:r2')
r_c1_1_c2_2_d_2_c_2 = a_flat.flattener.get_new_regime(
'b.d:r2 b.c1:r1 b.c2:r2 c:r2')
r_c1_2_c2_1_d_2_c_2 = a_flat.flattener.get_new_regime(
'b.d:r2 b.c1:r2 b.c2:r1 c:r2')
r_c1_2_c2_2_d_2_c_2 = a_flat.flattener.get_new_regime(
'b.d:r2 b.c1:r2 b.c2:r2 c:r2')
regimes = [
r_c1_1_c2_1_d_1_c_1, r_c1_1_c2_2_d_1_c_1, r_c1_2_c2_1_d_1_c_1,
r_c1_2_c2_2_d_1_c_1, r_c1_1_c2_1_d_2_c_1, r_c1_1_c2_2_d_2_c_1,
r_c1_2_c2_1_d_2_c_1, r_c1_2_c2_2_d_2_c_1, r_c1_1_c2_1_d_1_c_2,
r_c1_1_c2_2_d_1_c_2, r_c1_2_c2_1_d_1_c_2, r_c1_2_c2_2_d_1_c_2,
r_c1_1_c2_1_d_2_c_2, r_c1_1_c2_2_d_2_c_2, r_c1_2_c2_1_d_2_c_2,
r_c1_2_c2_2_d_2_c_2
]
self.assertEqual(len(set(regimes)), 16)
# Do we have the right number of on_events and on_conditions:
self.assertEqual(len(list(r_c1_1_c2_1_d_1_c_1.on_events)), 4)
self.assertEqual(len(list(r_c1_1_c2_1_d_1_c_1.on_conditions)), 4)
self.assertEqual(len(list(r_c1_1_c2_2_d_1_c_1.on_events)), 3)
self.assertEqual(len(list(r_c1_1_c2_2_d_1_c_1.on_conditions)), 4)
self.assertEqual(len(list(r_c1_2_c2_1_d_1_c_1.on_events)), 3)
self.assertEqual(len(list(r_c1_2_c2_1_d_1_c_1.on_conditions)), 4)
self.assertEqual(len(list(r_c1_2_c2_2_d_1_c_1.on_events)), 2)
self.assertEqual(len(list(r_c1_2_c2_2_d_1_c_1.on_conditions)), 4)
self.assertEqual(len(list(r_c1_1_c2_1_d_2_c_1.on_events)), 3)
self.assertEqual(len(list(r_c1_1_c2_1_d_2_c_1.on_conditions)), 4)
self.assertEqual(len(list(r_c1_1_c2_2_d_2_c_1.on_events)), 2)
self.assertEqual(len(list(r_c1_1_c2_2_d_2_c_1.on_conditions)), 4)
self.assertEqual(len(list(r_c1_2_c2_1_d_2_c_1.on_events)), 2)
self.assertEqual(len(list(r_c1_2_c2_1_d_2_c_1.on_conditions)), 4)
self.assertEqual(len(list(r_c1_2_c2_2_d_2_c_1.on_events)), 1)
self.assertEqual(len(list(r_c1_2_c2_2_d_2_c_1.on_conditions)), 4)
self.assertEqual(len(list(r_c1_1_c2_1_d_1_c_2.on_events)), 3)
self.assertEqual(len(list(r_c1_1_c2_1_d_1_c_2.on_conditions)), 4)
self.assertEqual(len(list(r_c1_1_c2_2_d_1_c_2.on_events)), 2)
self.assertEqual(len(list(r_c1_1_c2_2_d_1_c_2.on_conditions)), 4)
self.assertEqual(len(list(r_c1_2_c2_1_d_1_c_2.on_events)), 2)
self.assertEqual(len(list(r_c1_2_c2_1_d_1_c_2.on_conditions)), 4)
self.assertEqual(len(list(r_c1_2_c2_2_d_1_c_2.on_events)), 1)
self.assertEqual(len(list(r_c1_2_c2_2_d_1_c_2.on_conditions)), 4)
self.assertEqual(len(list(r_c1_1_c2_1_d_2_c_2.on_events)), 2)
self.assertEqual(len(list(r_c1_1_c2_1_d_2_c_2.on_conditions)), 4)
self.assertEqual(len(list(r_c1_1_c2_2_d_2_c_2.on_events)), 1)
self.assertEqual(len(list(r_c1_1_c2_2_d_2_c_2.on_conditions)), 4)
self.assertEqual(len(list(r_c1_2_c2_1_d_2_c_2.on_events)), 1)
self.assertEqual(len(list(r_c1_2_c2_1_d_2_c_2.on_conditions)), 4)
self.assertEqual(len(list(r_c1_2_c2_2_d_2_c_2.on_events)), 0)
self.assertEqual(len(list(r_c1_2_c2_2_d_2_c_2.on_conditions)), 4)
# All on_events return to thier same transition:
for r in a_flat.regimes:
for on_ev in r.on_events:
self.assertEquals(on_ev.target_regime, r)
# Check On-Event port names are remapped properly:
self.assertEqual(
set([ev.src_port_name for ev in r_c1_1_c2_1_d_1_c_1.on_events]),
set(['c_spikein', 'b_c1_spikein', 'b_c2_spikein', 'b_d_spikein']))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_1_c2_2_d_1_c_1.on_events]),
set(['c_spikein', 'b_c1_spikein', 'b_d_spikein']))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_2_c2_1_d_1_c_1.on_events]),
set(['c_spikein', 'b_c2_spikein', 'b_d_spikein']))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_2_c2_2_d_1_c_1.on_events]),
set(['c_spikein', 'b_d_spikein']))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_1_c2_1_d_2_c_1.on_events]),
set(['c_spikein', 'b_c1_spikein', 'b_c2_spikein']))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_1_c2_2_d_2_c_1.on_events]),
set([
'c_spikein',
'b_c1_spikein',
]))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_2_c2_1_d_2_c_1.on_events]),
set([
'c_spikein',
'b_c2_spikein',
]))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_2_c2_2_d_2_c_1.on_events]),
set(['c_spikein']))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_1_c2_1_d_1_c_2.on_events]),
set(['b_c1_spikein', 'b_c2_spikein', 'b_d_spikein']))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_1_c2_2_d_1_c_2.on_events]),
set(['b_c1_spikein', 'b_d_spikein']))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_2_c2_1_d_1_c_2.on_events]),
set(['b_c2_spikein', 'b_d_spikein']))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_2_c2_2_d_1_c_2.on_events]),
set(['b_d_spikein']))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_1_c2_1_d_2_c_2.on_events]),
set(['b_c1_spikein', 'b_c2_spikein']))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_1_c2_2_d_2_c_2.on_events]),
set([
'b_c1_spikein',
]))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_2_c2_1_d_2_c_2.on_events]),
set([
'b_c2_spikein',
]))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_2_c2_2_d_2_c_2.on_events]),
set([]))
# ToDo: Check the OnConditions:
# - Ports & Parameters:
self.assertEqual(
set(a_flat.query.analog_ports_map.keys()),
set([
'b_c1_C1', 'b_c1_C2', 'b_c2_C1', 'b_c2_C2', 'b_d_dIn2',
'b_d_D1', 'b_d_D2', 'c_cIn1', 'c_cIn2', 'c_C1', 'c_C2'
]))
self.assertEqual(
set(a_flat.query.event_ports_map.keys()),
set([
'b_c1_spikein',
'b_c1_emit',
'b_c1_c_emit',
'b_c2_spikein',
'b_c2_emit',
'b_c2_c_emit',
'b_d_spikein',
'b_d_emit',
'b_d_d_emit',
'c_spikein',
'c_emit',
'c_c_emit',
]))
self.assertEqual(
set(a_flat.query.parameters_map.keys()),
set([
'c_cp1',
'c_cp2',
'b_c1_cp1',
'b_c1_cp2',
'b_c2_cp1',
'b_c2_cp2',
'b_d_dp1',
'b_d_dp2',
]))
self.assertEqual(set(a_flat.state_variables_map.keys()),
set(['b_c1_SV1', 'b_c2_SV1', 'b_d_SV1', 'c_SV1']))
# Back-sub everything - then do we get the correct port mappings:
a_flat.backsub_all()
self.assertEqual(set(a_flat.aliases_map['b_c2_C4'].rhs_atoms),
set(['b_c1_cp1']))
self.assertEqual(set(a_flat.aliases_map['b_c1_C2'].rhs_atoms),
set(['b_c2_cp1']))
self.assertEqual(set(a_flat.aliases_map['b_c1_C4'].rhs_atoms),
set(['b_c1_cp1']))
self.assertEqual(set(a_flat.aliases_map['b_c2_C2'].rhs_atoms),
set(['b_c1_cp1']))
self.assertEqual(set(a_flat.aliases_map['b_d_D2'].rhs_atoms),
set(['b_c2_cp1', 'b_d_dp2']))
def func_test(self):
emitter = ComponentClass(
name='EventEmitter',
parameters=['rate'],
regimes=[
Regime(transitions=On(
't > tchange',
do=[
OutputEvent('emit'),
'tchange=t + random.exponential(1/rate) '
])),
])
ev_based_cc = ComponentClass(
name='EventBasedCurrentClass',
parameters=['dur', 'i'],
analog_ports=[SendPort('I')],
regimes=[
Regime(transitions=[
On('inputevent', do=['I=i', 'tchange = t']),
On('t>tchange + dur', do=['I=0', 'tchange=t'])
])
])
pulsing_emitter = ComponentClass(name='pulsing_cc',
subnodes={
'evs': emitter,
'cc': ev_based_cc
},
portconnections=[('evs.emit',
'cc.inputevent')])
nrn = ComponentClass(
name='LeakyNeuron',
parameters=['Cm', 'gL', 'E'],
regimes=[
Regime('dV/dt = (iInj + (E-V)*gL )/Cm'),
],
aliases=['iIn := iInj'],
analog_ports=[SendPort('V'),
ReducePort('iInj', reduce_op='+')],
)
combined_comp = ComponentClass(name='Comp1',
subnodes={
'nrn': nrn,
'cc1': pulsing_emitter,
'cc2': pulsing_emitter
},
portconnections=[
('cc1.cc.I', 'nrn.iInj'),
('cc2.cc.I', 'nrn.iInj')
])
combined_comp = 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 = flattening.ComponentFlattener.flatten_namespace_dict({
'cc1.cc.i':
13.8,
'cc1.cc.dur':
1,
'cc1.evs.rate':
110. / 1000.,
'cc2.cc.i':
20.8,
'cc2.cc.dur':
1.,
'cc2.evs.rate':
20. / 1000.,
'nrn.gL':
4.3,
'nrn.E':
-70
})
res = std_pynn_simulation(test_component=combined_comp,
parameters=parameters,
initial_values={},
synapse_components=[],
records=records,
sim_time=1000
# plot = False,
)
return
t, records = res
def check_trace(trace_name, time_period, exp_mean, exp_std=0):
t_indices = (t > time_period[0] + 1) & (t < time_period[1] - 1)
self.assertAlmostEqual(records[trace_name][t_indices].mean(),
exp_mean,
places=3)
self.assertAlmostEqual(records[trace_name][t_indices].std(),
exp_std,
places=3)
check_trace('cc1_cc_I', (00, 30), exp_mean=0.0)
check_trace('cc1_cc_I', (30, 40), exp_mean=13.8)
check_trace('cc1_cc_I', (40, 60), exp_mean=0.0)
check_trace('cc1_cc_I', (60, 70), exp_mean=13.8)
check_trace('cc1_cc_I', (70, 90), exp_mean=0.0)
check_trace('cc1_cc_I', (90, 100), exp_mean=13.8)
check_trace('cc2_cc_I', (00, 20), exp_mean=0.0)
check_trace('cc2_cc_I', (20, 25), exp_mean=20.8)
check_trace('cc2_cc_I', (25, 40), exp_mean=0.0)
check_trace('cc2_cc_I', (40, 45), exp_mean=20.8)
check_trace('cc2_cc_I', (45, 60), exp_mean=0.0)
check_trace('cc2_cc_I', (60, 65), exp_mean=20.8)
check_trace('cc2_cc_I', (65, 80), exp_mean=0.0)
check_trace('cc2_cc_I', (80, 85), exp_mean=20.8)
check_trace('cc2_cc_I', (85, 100), exp_mean=0.0)
check_trace('nrn_iIn', (00, 20), exp_mean=0.0)
check_trace('nrn_iIn', (20, 25), exp_mean=20.8)
check_trace('nrn_iIn', (25, 30), exp_mean=0.0)
check_trace('nrn_iIn', (30, 40), exp_mean=13.8)
check_trace('nrn_iIn', (40, 45), exp_mean=20.8)
check_trace('nrn_iIn', (45, 60), exp_mean=0.0)
check_trace('nrn_iIn', (60, 65), exp_mean=34.6)
check_trace('nrn_iIn', (65, 70), exp_mean=13.8)
check_trace('nrn_iIn', (70, 80), exp_mean=0.0)
check_trace('nrn_iIn', (80, 85), exp_mean=20.8)
check_trace('nrn_iIn', (85, 90), exp_mean=0.0)
check_trace('nrn_iIn', (90, 100), exp_mean=13.8)
check_trace('nrn_V', (00 + 2, 20), exp_mean=(0.0 / 4.3) - 70)
check_trace('nrn_V', (20 + 2, 25), exp_mean=(20.8 / 4.3) - 70)
check_trace('nrn_V', (25 + 2, 30), exp_mean=(0.0 / 4.3) - 70)
check_trace('nrn_V', (30 + 2, 40), exp_mean=(13.8 / 4.3) - 70)
check_trace('nrn_V', (40 + 2, 45), exp_mean=(20.8 / 4.3) - 70)
check_trace('nrn_V', (45 + 2, 60), exp_mean=(0.0 / 4.3) - 70)
check_trace('nrn_V', (60 + 2, 65), exp_mean=(34.6 / 4.3) - 70)
check_trace('nrn_V', (65 + 2, 70), exp_mean=(13.8 / 4.3) - 70)
check_trace('nrn_V', (70 + 2, 80), exp_mean=(0.0 / 4.3) - 70)
check_trace('nrn_V', (80 + 2, 85), exp_mean=(20.8 / 4.3) - 70)
check_trace('nrn_V', (85 + 2, 90), exp_mean=(0.0 / 4.3) - 70)
check_trace('nrn_V', (90 + 2, 100), exp_mean=(13.8 / 4.3) - 70)
def __new__(cls, name, bases, dct):
import nineml.abstraction_layer as al
from nineml.abstraction_layer import flattening, writers, component_modifiers
import nest
#Extract Parameters Back out from Dict:
nineml_model = dct['nineml_model']
synapse_components = dct['synapse_components']
# Flatten the model:
assert isinstance(nineml_model, al.ComponentClass)
if nineml_model.is_flat():
flat_component = nineml_model
else:
flat_component = flattening.flatten( nineml_model,name )
# Make the substitutions:
flat_component.backsub_all()
#flat_component.backsub_aliases()
#flat_component.backsub_equations()
# Close any open reduce ports:
component_modifiers.ComponentModifier.close_all_reduce_ports(component = flat_component)
flat_component.short_description = "Auto-generated 9ML neuron model for PyNN.nest"
flat_component.long_description = "Auto-generated 9ML neuron model for PyNN.nest"
# Close any open reduce ports:
component_modifiers.ComponentModifier.close_all_reduce_ports(component = flat_component)
# synapse ports:
synapse_ports = []
for syn in synapse_components:
# get recv event ports
# TODO: model namespace look
#syn_component = nineml_model[syn.namespace]
syn_component = nineml_model.subnodes[syn.namespace]
recv_event_ports = list(syn_component.query.event_recv_ports)
# check there's only one
if len(recv_event_ports)!=1:
raise ValueError("A synapse component has multiple recv ports. Cannot dis-ambiguate")
synapse_ports.append(syn.namespace+'_'+recv_event_ports[0].name)
# New:
dct["combined_model"] = flat_component
# TODO: Override this with user layer
#default_values = ModelToSingleComponentReducer.flatten_namespace_dict( parameters )
dct["default_parameters"] = dict( (p.name, 1.0) for p in flat_component.parameters )
dct["default_initial_values"] = dict((s.name, 0.0) for s in flat_component.state_variables)
dct["synapse_types"] = [syn.namespace for syn in synapse_components]
dct["standard_receptor_type"] = (dct["synapse_types"] == ('excitatory', 'inhibitory'))
dct["injectable"] = True # need to determine this. How??
dct["conductance_based"] = True # how to determine this??
dct["model_name"] = name
dct["nest_model"] = name
# Recording from bindings:
dct["recordable"] = [port.name for port in flat_component.analog_ports] + ['spikes', 'regime']
# TODO bindings -> alias and support recording of them in nest template
#+ [binding.name for binding in flat_component.bindings]
dct["weight_variables"] = dict([ (syn.namespace,syn.namespace+'_'+syn.weight_connector )
for syn in synapse_components ])
logger.debug("Creating class '%s' with bases %s and dictionary %s" % (name, bases, dct))
# TODO: UL configuration of initial regime.
initial_regime = flat_component.regimes_map.keys()[0]
from nestbuilder import NestFileBuilder
nfb = NestFileBuilder( nest_classname = name,
component = flat_component,
synapse_ports = synapse_ports,
initial_regime = initial_regime,
initial_values = dct["default_initial_values"],
default_values = dct["default_parameters"],
)
nfb.compile_files()
nest.Install('mymodule')
return type.__new__(cls, name, bases, dct)
def t4():
print 'Loading Forth XML File (iaf-2coba-Model)'
print '----------------------------------------'
component = readers.XMLReader.read_component(
Join(tenml_dir, 'iaf_2coba.10ml'), component_name='iaf')
writers.XMLWriter.write(component, '/tmp/nineml_toxml4.xml', )
model = readers.XMLReader.read_component(Join(tenml_dir, 'iaf_2coba.10ml'))
from nineml.abstraction_layer.flattening import flatten
from nineml.abstraction_layer.component_modifiers import ComponentModifier
flatcomponent = flatten(model, componentname='iaf_2coba')
ComponentModifier.close_analog_port(component=flatcomponent, port_name='iaf_iSyn', value='0')
writers.XMLWriter.write(flatcomponent, '/tmp/nineml_out_iaf_2coba.9ml')
import pyNN.neuron as sim
from pyNN.utility import init_logging
init_logging(None, debug=True)
sim.setup(timestep=0.1, min_delay=0.1)
print 'Attempting to simulate From Model:'
print '----------------------------------'
celltype_cls = pyNNml.nineml_celltype_from_model(
name="iaf_2coba",
nineml_model=flatcomponent,
synapse_components=[
pyNNml.CoBaSyn(namespace='cobaExcit', weight_connector='q'),
pyNNml.CoBaSyn(namespace='cobaInhib', weight_connector='q'),
]
)
parameters = {
'iaf.cm': 1.0,
'iaf.gl': 50.0,
'iaf.taurefrac': 5.0,
'iaf.vrest': -65.0,
'iaf.vreset': -65.0,
'iaf.vthresh': -50.0,
'cobaExcit.tau': 2.0,
'cobaInhib.tau': 5.0,
'cobaExcit.vrev': 0.0,
'cobaInhib.vrev': -70.0,
}
parameters = ComponentFlattener.flatten_namespace_dict(parameters)
cells = sim.Population(1, celltype_cls, parameters)
cells.initialize('iaf_V', parameters['iaf_vrest'])
cells.initialize('tspike', -1e99) # neuron not refractory at start
cells.initialize('regime', 1002) # temporary hack
input = sim.Population(2, sim.SpikeSourcePoisson, {'rate': 100})
connector = sim.OneToOneConnector(weights=1.0, delays=0.5)
conn = [sim.Projection(input[0:1], cells, connector, target='cobaExcit'),
sim.Projection(input[1:2], cells, connector, target='cobaInhib')]
cells._record('iaf_V')
cells._record('cobaExcit_g')
cells._record('cobaInhib_g')
cells._record('cobaExcit_I')
cells._record('cobaInhib_I')
cells.record()
sim.run(100.0)
cells.recorders['iaf_V'].write("Results/nineml_neuron.V", filter=[cells[0]])
cells.recorders['cobaExcit_g'].write("Results/nineml_neuron.g_exc", filter=[cells[0]])
cells.recorders['cobaInhib_g'].write("Results/nineml_neuron.g_inh", filter=[cells[0]])
cells.recorders['cobaExcit_I'].write("Results/nineml_neuron.g_exc", filter=[cells[0]])
cells.recorders['cobaInhib_I'].write("Results/nineml_neuron.g_inh", filter=[cells[0]])
t = cells.recorders['iaf_V'].get()[:, 1]
v = cells.recorders['iaf_V'].get()[:, 2]
gInh = cells.recorders['cobaInhib_g'].get()[:, 2]
gExc = cells.recorders['cobaExcit_g'].get()[:, 2]
IInh = cells.recorders['cobaInhib_I'].get()[:, 2]
IExc = cells.recorders['cobaExcit_I'].get()[:, 2]
import pylab
pylab.subplot(311)
pylab.ylabel('Voltage')
pylab.plot(t, v)
pylab.subplot(312)
pylab.ylabel('Conductance')
pylab.plot(t, gInh)
pylab.plot(t, gExc)
pylab.subplot(313)
pylab.ylabel('Current')
pylab.plot(t, IInh)
pylab.plot(t, IExc)
pylab.suptitle("From Tree-Model Pathway")
pylab.show()
sim.end()
import nineml.abstraction_layer as nineml import os #import nineml.models from nineml.abstraction_layer.example_models import get_hierachical_iaf_2coba #from nineml.abstraction_layer.models import reduce_to_single_component, ModelToSingleComponentReducer from nineml.abstraction_layer.flattening import flatten, ComponentFlattener from nineml.abstraction_layer.writers import dump_reduced from nineml.abstraction_layer.componentmodifiers import ComponentModifier nest_classname = "iaf_cond_exp_9ml" iaf_cond_exp_9ML_reduced = flatten( get_hierachical_iaf_2coba(), componentname=nest_classname ) iaf_cond_exp_9ML_reduced.backsub_aliases() iaf_cond_exp_9ML_reduced.backsub_equations() ComponentModifier.close_all_reduce_ports(component=iaf_cond_exp_9ML_reduced) dump_reduced(iaf_cond_exp_9ML_reduced,'reduced.txt') iaf_cond_exp_9ML_reduced.long_description = """ Long description of the iaf_cond_exp ... Author: Eilif Muller, Ecublens, 2011 """ iaf_cond_exp_9ML_reduced.short_description = "Standard integrate and fire with exponential conductance based synapses"
def test_Flattening4(self):
c = ComponentClass(
name='C',
aliases=['C1:=cp1', 'C2 := cIn1', 'C3 := SV1', 'C4:=cIn2'],
regimes=[
Regime(
'dSV1/dt = -SV1/cp2',
transitions=[On('SV1>cp1', do=[OutputEvent('emit')]),
On('spikein', do=[OutputEvent('c_emit')])],
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 = ComponentClass(
name='D',
aliases=['D1:=dp1', 'D2 := dIn1 + dp2', 'D3 := SV1'],
regimes=[
Regime(
'dSV1/dt = -SV1/dp2',
transitions=[On('SV1>dp1', do=[OutputEvent('emit')]),
On('spikein', do=[OutputEvent('d_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']
)
# Test Cloner, 2 levels of hierachy
# ------------------------------ #
# Everything should be as before:
b = ComponentClass(name='B',
subnodes={'c1': c, 'c2': c, 'd': d},
portconnections=[('c1.C1', 'c2.cIn2'),
('c2.C1', 'c1.cIn1')],
)
a = ComponentClass(name='A',
subnodes={'b': b, 'c': c},
portconnections=[('b.c1.C1', 'b.c1.cIn2'),
('b.c1.C1', 'b.c2.cIn1'),
('b.c1.C2', 'b.d.dIn1')]
)
a_flat = flattening.flatten(a)
# Name
self.assertEqual(a_flat.name, 'A')
# Aliases
self.assertEqual(
set(a_flat.aliases_map.keys()),
set(['b_c1_C1', 'b_c1_C2', 'b_c1_C3', 'b_c1_C4',
'b_c2_C1', 'b_c2_C2', 'b_c2_C3', 'b_c2_C4',
'b_d_D1', 'b_d_D2', 'b_d_D3',
'c_C1', 'c_C2', 'c_C3', 'c_C4']))
# - Regimes and Transitions:
self.assertEqual(len(a_flat.regimes_map), 16)
r_c1_1_c2_1_d_1_c_1 = a_flat.flattener.get_new_regime('b.d:r1 b.c1:r1 b.c2:r1 c:r1')
r_c1_1_c2_2_d_1_c_1 = a_flat.flattener.get_new_regime('b.d:r1 b.c1:r1 b.c2:r2 c:r1')
r_c1_2_c2_1_d_1_c_1 = a_flat.flattener.get_new_regime('b.d:r1 b.c1:r2 b.c2:r1 c:r1')
r_c1_2_c2_2_d_1_c_1 = a_flat.flattener.get_new_regime('b.d:r1 b.c1:r2 b.c2:r2 c:r1')
r_c1_1_c2_1_d_2_c_1 = a_flat.flattener.get_new_regime('b.d:r2 b.c1:r1 b.c2:r1 c:r1')
r_c1_1_c2_2_d_2_c_1 = a_flat.flattener.get_new_regime('b.d:r2 b.c1:r1 b.c2:r2 c:r1')
r_c1_2_c2_1_d_2_c_1 = a_flat.flattener.get_new_regime('b.d:r2 b.c1:r2 b.c2:r1 c:r1')
r_c1_2_c2_2_d_2_c_1 = a_flat.flattener.get_new_regime('b.d:r2 b.c1:r2 b.c2:r2 c:r1')
r_c1_1_c2_1_d_1_c_2 = a_flat.flattener.get_new_regime('b.d:r1 b.c1:r1 b.c2:r1 c:r2')
r_c1_1_c2_2_d_1_c_2 = a_flat.flattener.get_new_regime('b.d:r1 b.c1:r1 b.c2:r2 c:r2')
r_c1_2_c2_1_d_1_c_2 = a_flat.flattener.get_new_regime('b.d:r1 b.c1:r2 b.c2:r1 c:r2')
r_c1_2_c2_2_d_1_c_2 = a_flat.flattener.get_new_regime('b.d:r1 b.c1:r2 b.c2:r2 c:r2')
r_c1_1_c2_1_d_2_c_2 = a_flat.flattener.get_new_regime('b.d:r2 b.c1:r1 b.c2:r1 c:r2')
r_c1_1_c2_2_d_2_c_2 = a_flat.flattener.get_new_regime('b.d:r2 b.c1:r1 b.c2:r2 c:r2')
r_c1_2_c2_1_d_2_c_2 = a_flat.flattener.get_new_regime('b.d:r2 b.c1:r2 b.c2:r1 c:r2')
r_c1_2_c2_2_d_2_c_2 = a_flat.flattener.get_new_regime('b.d:r2 b.c1:r2 b.c2:r2 c:r2')
regimes = [
r_c1_1_c2_1_d_1_c_1,
r_c1_1_c2_2_d_1_c_1,
r_c1_2_c2_1_d_1_c_1,
r_c1_2_c2_2_d_1_c_1,
r_c1_1_c2_1_d_2_c_1,
r_c1_1_c2_2_d_2_c_1,
r_c1_2_c2_1_d_2_c_1,
r_c1_2_c2_2_d_2_c_1,
r_c1_1_c2_1_d_1_c_2,
r_c1_1_c2_2_d_1_c_2,
r_c1_2_c2_1_d_1_c_2,
r_c1_2_c2_2_d_1_c_2,
r_c1_1_c2_1_d_2_c_2,
r_c1_1_c2_2_d_2_c_2,
r_c1_2_c2_1_d_2_c_2,
r_c1_2_c2_2_d_2_c_2]
self.assertEqual(len(set(regimes)), 16)
# Do we have the right number of on_events and on_conditions:
self.assertEqual(len(list(r_c1_1_c2_1_d_1_c_1.on_events)), 4)
self.assertEqual(len(list(r_c1_1_c2_1_d_1_c_1.on_conditions)), 4)
self.assertEqual(len(list(r_c1_1_c2_2_d_1_c_1.on_events)), 3)
self.assertEqual(len(list(r_c1_1_c2_2_d_1_c_1.on_conditions)), 4)
self.assertEqual(len(list(r_c1_2_c2_1_d_1_c_1.on_events)), 3)
self.assertEqual(len(list(r_c1_2_c2_1_d_1_c_1.on_conditions)), 4)
self.assertEqual(len(list(r_c1_2_c2_2_d_1_c_1.on_events)), 2)
self.assertEqual(len(list(r_c1_2_c2_2_d_1_c_1.on_conditions)), 4)
self.assertEqual(len(list(r_c1_1_c2_1_d_2_c_1.on_events)), 3)
self.assertEqual(len(list(r_c1_1_c2_1_d_2_c_1.on_conditions)), 4)
self.assertEqual(len(list(r_c1_1_c2_2_d_2_c_1.on_events)), 2)
self.assertEqual(len(list(r_c1_1_c2_2_d_2_c_1.on_conditions)), 4)
self.assertEqual(len(list(r_c1_2_c2_1_d_2_c_1.on_events)), 2)
self.assertEqual(len(list(r_c1_2_c2_1_d_2_c_1.on_conditions)), 4)
self.assertEqual(len(list(r_c1_2_c2_2_d_2_c_1.on_events)), 1)
self.assertEqual(len(list(r_c1_2_c2_2_d_2_c_1.on_conditions)), 4)
self.assertEqual(len(list(r_c1_1_c2_1_d_1_c_2.on_events)), 3)
self.assertEqual(len(list(r_c1_1_c2_1_d_1_c_2.on_conditions)), 4)
self.assertEqual(len(list(r_c1_1_c2_2_d_1_c_2.on_events)), 2)
self.assertEqual(len(list(r_c1_1_c2_2_d_1_c_2.on_conditions)), 4)
self.assertEqual(len(list(r_c1_2_c2_1_d_1_c_2.on_events)), 2)
self.assertEqual(len(list(r_c1_2_c2_1_d_1_c_2.on_conditions)), 4)
self.assertEqual(len(list(r_c1_2_c2_2_d_1_c_2.on_events)), 1)
self.assertEqual(len(list(r_c1_2_c2_2_d_1_c_2.on_conditions)), 4)
self.assertEqual(len(list(r_c1_1_c2_1_d_2_c_2.on_events)), 2)
self.assertEqual(len(list(r_c1_1_c2_1_d_2_c_2.on_conditions)), 4)
self.assertEqual(len(list(r_c1_1_c2_2_d_2_c_2.on_events)), 1)
self.assertEqual(len(list(r_c1_1_c2_2_d_2_c_2.on_conditions)), 4)
self.assertEqual(len(list(r_c1_2_c2_1_d_2_c_2.on_events)), 1)
self.assertEqual(len(list(r_c1_2_c2_1_d_2_c_2.on_conditions)), 4)
self.assertEqual(len(list(r_c1_2_c2_2_d_2_c_2.on_events)), 0)
self.assertEqual(len(list(r_c1_2_c2_2_d_2_c_2.on_conditions)), 4)
# All on_events return to thier same transition:
for r in a_flat.regimes:
for on_ev in r.on_events:
self.assertEquals(on_ev.target_regime, r)
# Check On-Event port names are remapped properly:
self.assertEqual(set([ev.src_port_name for ev in r_c1_1_c2_1_d_1_c_1.on_events]), set(
['c_spikein', 'b_c1_spikein', 'b_c2_spikein', 'b_d_spikein']))
self.assertEqual(set([ev.src_port_name for ev in r_c1_1_c2_2_d_1_c_1.on_events]), set(
['c_spikein', 'b_c1_spikein', 'b_d_spikein']))
self.assertEqual(set([ev.src_port_name for ev in r_c1_2_c2_1_d_1_c_1.on_events]), set(
['c_spikein', 'b_c2_spikein', 'b_d_spikein']))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_2_c2_2_d_1_c_1.on_events]), set(['c_spikein', 'b_d_spikein']))
self.assertEqual(set([ev.src_port_name for ev in r_c1_1_c2_1_d_2_c_1.on_events]), set(
['c_spikein', 'b_c1_spikein', 'b_c2_spikein']))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_1_c2_2_d_2_c_1.on_events]), set(['c_spikein', 'b_c1_spikein', ]))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_2_c2_1_d_2_c_1.on_events]), set(['c_spikein', 'b_c2_spikein', ]))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_2_c2_2_d_2_c_1.on_events]), set(['c_spikein']))
self.assertEqual(set([ev.src_port_name for ev in r_c1_1_c2_1_d_1_c_2.on_events]), set(
['b_c1_spikein', 'b_c2_spikein', 'b_d_spikein']))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_1_c2_2_d_1_c_2.on_events]), set(['b_c1_spikein', 'b_d_spikein']))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_2_c2_1_d_1_c_2.on_events]), set(['b_c2_spikein', 'b_d_spikein']))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_2_c2_2_d_1_c_2.on_events]), set(['b_d_spikein']))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_1_c2_1_d_2_c_2.on_events]), set(['b_c1_spikein', 'b_c2_spikein']))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_1_c2_2_d_2_c_2.on_events]), set(['b_c1_spikein', ]))
self.assertEqual(
set([ev.src_port_name for ev in r_c1_2_c2_1_d_2_c_2.on_events]), set(['b_c2_spikein', ]))
self.assertEqual(set([ev.src_port_name for ev in r_c1_2_c2_2_d_2_c_2.on_events]), set([]))
# ToDo: Check the OnConditions:
# - Ports & Parameters:
self.assertEqual(
set(a_flat.query.analog_ports_map.keys()),
set(['b_c1_C1', 'b_c1_C2',
'b_c2_C1', 'b_c2_C2',
'b_d_dIn2', 'b_d_D1', 'b_d_D2',
'c_cIn1', 'c_cIn2', 'c_C1', 'c_C2']))
self.assertEqual(
set(a_flat.query.event_ports_map.keys()),
set(['b_c1_spikein', 'b_c1_emit', 'b_c1_c_emit',
'b_c2_spikein', 'b_c2_emit', 'b_c2_c_emit',
'b_d_spikein', 'b_d_emit', 'b_d_d_emit',
'c_spikein', 'c_emit', 'c_c_emit', ]))
self.assertEqual(
set(a_flat.query.parameters_map.keys()),
set(['c_cp1', 'c_cp2',
'b_c1_cp1', 'b_c1_cp2',
'b_c2_cp1', 'b_c2_cp2',
'b_d_dp1', 'b_d_dp2', ]))
self.assertEqual(
set(a_flat.state_variables_map.keys()),
set(['b_c1_SV1', 'b_c2_SV1', 'b_d_SV1', 'c_SV1']))
# Back-sub everything - then do we get the correct port mappings:
a_flat.backsub_all()
self.assertEqual(
set(a_flat.aliases_map['b_c2_C4'].rhs_atoms),
set(['b_c1_cp1']))
self.assertEqual(
set(a_flat.aliases_map['b_c1_C2'].rhs_atoms),
set(['b_c2_cp1']))
self.assertEqual(
set(a_flat.aliases_map['b_c1_C4'].rhs_atoms),
set(['b_c1_cp1']))
self.assertEqual(
set(a_flat.aliases_map['b_c2_C2'].rhs_atoms),
set(['b_c1_cp1']))
self.assertEqual(
set(a_flat.aliases_map['b_d_D2'].rhs_atoms),
set(['b_c2_cp1', 'b_d_dp2']))
def __new__(cls, name, bases, dct):
import nineml.abstraction_layer as al
from nineml.abstraction_layer import flattening, writers, component_modifiers
import nest
# Extract Parameters Back out from Dict:
nineml_model = dct["nineml_model"]
synapse_components = dct["synapse_components"]
# Flatten the model:
assert isinstance(nineml_model, al.ComponentClass)
if nineml_model.is_flat():
flat_component = nineml_model
else:
flat_component = flattening.flatten(nineml_model, name)
# Make the substitutions:
flat_component.backsub_all()
# flat_component.backsub_aliases()
# flat_component.backsub_equations()
# Close any open reduce ports:
component_modifiers.ComponentModifier.close_all_reduce_ports(component=flat_component)
flat_component.short_description = "Auto-generated 9ML neuron model for PyNN.nest"
flat_component.long_description = "Auto-generated 9ML neuron model for PyNN.nest"
# Close any open reduce ports:
component_modifiers.ComponentModifier.close_all_reduce_ports(component=flat_component)
# synapse ports:
synapse_ports = []
for syn in synapse_components:
# get recv event ports
# TODO: model namespace look
# syn_component = nineml_model[syn.namespace]
syn_component = nineml_model.subnodes[syn.namespace]
recv_event_ports = list(syn_component.query.event_recv_ports)
# check there's only one
if len(recv_event_ports) != 1:
raise ValueError, "A synapse component has multiple recv ports. Cannot dis-ambiguate"
synapse_ports.append(syn.namespace + "_" + recv_event_ports[0].name)
# New:
dct["combined_model"] = flat_component
# TODO: Override this with user layer
# default_values = ModelToSingleComponentReducer.flatten_namespace_dict( parameters )
dct["default_parameters"] = dict((p.name, 1.0) for p in flat_component.parameters)
dct["default_initial_values"] = dict((s.name, 0.0) for s in flat_component.state_variables)
dct["synapse_types"] = [syn.namespace for syn in synapse_components]
dct["standard_receptor_type"] = dct["synapse_types"] == ("excitatory", "inhibitory")
dct["injectable"] = True # need to determine this. How??
dct["conductance_based"] = True # how to determine this??
dct["model_name"] = name
dct["nest_model"] = name
# Recording from bindings:
dct["recordable"] = [port.name for port in flat_component.analog_ports] + ["spikes", "regime"]
# TODO bindings -> alias and support recording of them in nest template
# + [binding.name for binding in flat_component.bindings]
dct["weight_variables"] = dict(
[(syn.namespace, syn.namespace + "_" + syn.weight_connector) for syn in synapse_components]
)
logger.debug("Creating class '%s' with bases %s and dictionary %s" % (name, bases, dct))
# TODO: UL configuration of initial regime.
initial_regime = flat_component.regimes_map.keys()[0]
from nestbuilder import NestFileBuilder
nfb = NestFileBuilder(
nest_classname=name,
component=flat_component,
synapse_ports=synapse_ports,
initial_regime=initial_regime,
initial_values=dct["default_initial_values"],
default_values=dct["default_parameters"],
)
nfb.compile_files()
nest.Install("mymodule")
return type.__new__(cls, name, bases, dct)
"""
import nineml.abstraction_layer as nineml
import os
#import nineml.models
from nineml.abstraction_layer.example_models import get_hierachical_iaf_2coba
#from nineml.abstraction_layer.models import reduce_to_single_component, ModelToSingleComponentReducer
from nineml.abstraction_layer.flattening import flatten, ComponentFlattener
from nineml.abstraction_layer.writers import dump_reduced
from nineml.abstraction_layer.componentmodifiers import ComponentModifier
nest_classname = "iaf_cond_exp_9ml"
iaf_cond_exp_9ML_reduced = flatten(get_hierachical_iaf_2coba(),
componentname=nest_classname)
iaf_cond_exp_9ML_reduced.backsub_aliases()
iaf_cond_exp_9ML_reduced.backsub_equations()
ComponentModifier.close_all_reduce_ports(component=iaf_cond_exp_9ML_reduced)
dump_reduced(iaf_cond_exp_9ML_reduced, 'reduced.txt')
iaf_cond_exp_9ML_reduced.long_description = """
Long description of the iaf_cond_exp ...
Author: Eilif Muller, Ecublens, 2011
"""
iaf_cond_exp_9ML_reduced.short_description = "Standard integrate and fire with exponential conductance based synapses"
# Things we need to know which should come from the user layer
synapse_ports = ['cobaExcit_spikeinput', 'cobaInhib_spikeinput']