def test_coba_synapse():
nineml_component = TestableComponent('coba_synapse')()
if not nineml_component:
raise RuntimeError('Cannot load NineML component')
timeHorizon = 1
reportingInterval = 0.001
parameters = {
'CobaSyn.q': 4.0E-9,
'CobaSyn.tau': 0.005,
'CobaSyn.vrev': 0.0
}
initial_conditions = {
'CobaSyn.g': 1E-8,
}
analog_ports_expressions = {'CobaSyn.V': -0.050}
event_ports_expressions = {
'CobaSyn.spikeinput':
'' #'0.05, 0.10, 0.20, 0.30, 0.40, 0.50, 0.60, 0.70, 0.80, 0.90'
}
active_regimes = {'CobaSyn': 'cobadefaultregime'}
variables_to_report = {'CobaSyn.I': True}
inspector = nineml_component_inspector()
inspector.inspect(nineml_component,
timeHorizon=timeHorizon,
reportingInterval=reportingInterval,
parameters=parameters,
initial_conditions=initial_conditions,
active_regimes=active_regimes,
analog_ports_expressions=analog_ports_expressions,
event_ports_expressions=event_ports_expressions,
variables_to_report=variables_to_report)
results = inspector.showQtGUI()
return results, inspector
def test_iaf():
nineml_component = TestableComponent('iaf')()
if not nineml_component:
raise RuntimeError('Cannot load NineML component')
timeHorizon = 1
reportingInterval = 0.001
parameters = {
'iaf.cm': 0.2E-9,
'iaf.gl': 1E-8,
'iaf.taurefrac': 0.001,
'iaf.vreset': -0.060,
'iaf.vrest': -0.060,
'iaf.vthresh': -0.040
}
initial_conditions = {'iaf.V': -0.050, 'iaf.tspike': -1.0}
analog_ports_expressions = {'iaf.ISyn': 0.0}
event_ports_expressions = {}
active_regimes = {'iaf': 'subthresholdregime'}
variables_to_report = {'iaf.V': True}
inspector = nineml_component_inspector()
inspector.inspect(nineml_component,
timeHorizon=timeHorizon,
reportingInterval=reportingInterval,
parameters=parameters,
initial_conditions=initial_conditions,
active_regimes=active_regimes,
analog_ports_expressions=analog_ports_expressions,
event_ports_expressions=event_ports_expressions,
variables_to_report=variables_to_report)
results = inspector.showQtGUI()
return results, inspector
def test_Izhikevich():
nineml_component = TestableComponent('izhikevich')()
if not nineml_component:
raise RuntimeError('Cannot load NineML component')
timeHorizon = 1
reportingInterval = 0.001
parameters = {
"Izhikevich.a": 0.02,
"Izhikevich.b": 0.2,
"Izhikevich.c": -0.05,
"Izhikevich.d": 2.0,
"Izhikevich.theta": 0.03
}
initial_conditions = {"Izhikevich.U": 0.0, "Izhikevich.V": -0.07}
analog_ports_expressions = {"Izhikevich.Isyn": "0.1"}
event_ports_expressions = {}
active_regimes = {}
variables_to_report = {'Izhikevich.U': True, 'Izhikevich.V': True}
inspector = nineml_component_inspector()
inspector.inspect(nineml_component,
timeHorizon=timeHorizon,
reportingInterval=reportingInterval,
parameters=parameters,
initial_conditions=initial_conditions,
active_regimes=active_regimes,
analog_ports_expressions=analog_ports_expressions,
event_ports_expressions=event_ports_expressions,
variables_to_report=variables_to_report)
results = inspector.showQtGUI()
return results, inspector
def test_other(component_name):
nineml_component = TestableComponent(component_name)()
if not nineml_component:
raise RuntimeError('Cannot load NineML component {0}'.format(component_name))
inspector = nineml_component_inspector()
inspector.inspect(nineml_component)
results = inspector.showQtGUI()
return results, inspector
def test_other(component_name):
nineml_component = TestableComponent(component_name)()
if not nineml_component:
raise RuntimeError(
'Cannot load NineML component {0}'.format(component_name))
inspector = nineml_component_inspector()
inspector.inspect(nineml_component)
results = inspector.showQtGUI()
return results, inspector
def test_hierachical_iaf_1coba():
nineml_component = TestableComponent('hierachical_iaf_1coba')()
if not nineml_component:
raise RuntimeError('Cannot load NineML component')
timeHorizon = 1.0
reportingInterval = 0.001
initial_conditions = {
"iaf_1coba.iaf.tspike": -1.0,
"iaf_1coba.iaf.V": -0.060,
"iaf_1coba.cobaExcit.g": 0.0
}
parameters = {
"iaf_1coba.iaf.gl": 1E-8,
"iaf_1coba.iaf.vreset": -0.060,
"iaf_1coba.iaf.taurefrac": 0.001,
"iaf_1coba.iaf.vthresh": -0.040,
"iaf_1coba.iaf.vrest": -0.060,
"iaf_1coba.iaf.cm": 0.2E-9,
"iaf_1coba.cobaExcit.vrev": 0.0,
"iaf_1coba.cobaExcit.q": 4.0E-9,
"iaf_1coba.cobaExcit.tau": 0.005
}
variables_to_report = {
"iaf_1coba.cobaExcit.I": True,
"iaf_1coba.iaf.V": True
}
event_ports_expressions = {
"iaf_1coba.cobaExcit.spikeinput":
"0.05, 0.10, 0.20, 0.30, 0.40, 0.50, 0.60, 0.70, 0.80, 0.90"
}
active_regimes = {
"iaf_1coba.cobaExcit": "cobadefaultregime",
"iaf_1coba.iaf": "subthresholdregime"
}
analog_ports_expressions = {}
inspector = nineml_component_inspector()
inspector.inspect(nineml_component,
timeHorizon=timeHorizon,
reportingInterval=reportingInterval,
parameters=parameters,
initial_conditions=initial_conditions,
active_regimes=active_regimes,
analog_ports_expressions=analog_ports_expressions,
event_ports_expressions=event_ports_expressions,
variables_to_report=variables_to_report)
results = inspector.showQtGUI()
return results, inspector
def test_hierachical_iaf_1coba():
nineml_component = TestableComponent('hierachical_iaf_1coba')()
if not nineml_component:
raise RuntimeError('Cannot load NineML component')
timeHorizon = 1.0
reportingInterval = 0.001
initial_conditions = {
"iaf_1coba.iaf.tspike": -1.0,
"iaf_1coba.iaf.V": -0.060,
"iaf_1coba.cobaExcit.g": 0.0
}
parameters = {
"iaf_1coba.iaf.gl": 1E-8,
"iaf_1coba.iaf.vreset": -0.060,
"iaf_1coba.iaf.taurefrac": 0.001,
"iaf_1coba.iaf.vthresh": -0.040,
"iaf_1coba.iaf.vrest": -0.060,
"iaf_1coba.iaf.cm": 0.2E-9,
"iaf_1coba.cobaExcit.vrev": 0.0,
"iaf_1coba.cobaExcit.q": 4.0E-9,
"iaf_1coba.cobaExcit.tau": 0.005
}
variables_to_report = {
"iaf_1coba.cobaExcit.I": True,
"iaf_1coba.iaf.V": True
}
event_ports_expressions = {
"iaf_1coba.cobaExcit.spikeinput": "0.05, 0.10, 0.20, 0.30, 0.40, 0.50, 0.60, 0.70, 0.80, 0.90"
}
active_regimes = {
"iaf_1coba.cobaExcit": "cobadefaultregime",
"iaf_1coba.iaf": "subthresholdregime"
}
analog_ports_expressions = {}
inspector = nineml_component_inspector()
inspector.inspect(nineml_component, timeHorizon = timeHorizon,
reportingInterval = reportingInterval,
parameters = parameters,
initial_conditions = initial_conditions,
active_regimes = active_regimes,
analog_ports_expressions = analog_ports_expressions,
event_ports_expressions = event_ports_expressions,
variables_to_report = variables_to_report)
results = inspector.showQtGUI()
return results, inspector
def test_iaf():
nineml_component = TestableComponent('iaf')()
if not nineml_component:
raise RuntimeError('Cannot load NineML component')
timeHorizon = 1
reportingInterval = 0.001
parameters = {
'iaf.cm' : 0.2E-9,
'iaf.gl' : 1E-8,
'iaf.taurefrac' : 0.001,
'iaf.vreset' : -0.060,
'iaf.vrest' : -0.060,
'iaf.vthresh' : -0.040
}
initial_conditions = {
'iaf.V' : -0.050,
'iaf.tspike' : -1.0
}
analog_ports_expressions = {
'iaf.ISyn' : 0.0
}
event_ports_expressions = {}
active_regimes = {
'iaf' : 'subthresholdregime'
}
variables_to_report = {
'iaf.V' : True
}
inspector = nineml_component_inspector()
inspector.inspect(nineml_component, timeHorizon = timeHorizon,
reportingInterval = reportingInterval,
parameters = parameters,
initial_conditions = initial_conditions,
active_regimes = active_regimes,
analog_ports_expressions = analog_ports_expressions,
event_ports_expressions = event_ports_expressions,
variables_to_report = variables_to_report)
results = inspector.showQtGUI()
return results, inspector
def test_Izhikevich():
nineml_component = TestableComponent('izhikevich')()
if not nineml_component:
raise RuntimeError('Cannot load NineML component')
timeHorizon = 1
reportingInterval = 0.001
parameters = {
"Izhikevich.a": 0.02,
"Izhikevich.b": 0.2,
"Izhikevich.c": -0.05,
"Izhikevich.d": 2.0,
"Izhikevich.theta": 0.03
}
initial_conditions = {
"Izhikevich.U": 0.0,
"Izhikevich.V": -0.07
}
analog_ports_expressions = {
"Izhikevich.Isyn": "0.1"
}
event_ports_expressions = {}
active_regimes = {}
variables_to_report = {
'Izhikevich.U' : True,
'Izhikevich.V' : True
}
inspector = nineml_component_inspector()
inspector.inspect(nineml_component, timeHorizon = timeHorizon,
reportingInterval = reportingInterval,
parameters = parameters,
initial_conditions = initial_conditions,
active_regimes = active_regimes,
analog_ports_expressions = analog_ports_expressions,
event_ports_expressions = event_ports_expressions,
variables_to_report = variables_to_report)
results = inspector.showQtGUI()
return results, inspector
def test_coba_synapse():
nineml_component = TestableComponent('coba_synapse')()
if not nineml_component:
raise RuntimeError('Cannot load NineML component')
timeHorizon = 1
reportingInterval = 0.001
parameters = {
'CobaSyn.q' : 4.0E-9,
'CobaSyn.tau' : 0.005,
'CobaSyn.vrev' : 0.0
}
initial_conditions = {
'CobaSyn.g' : 1E-8,
}
analog_ports_expressions = {
'CobaSyn.V' : -0.050
}
event_ports_expressions = {
'CobaSyn.spikeinput' : '' #'0.05, 0.10, 0.20, 0.30, 0.40, 0.50, 0.60, 0.70, 0.80, 0.90'
}
active_regimes = {
'CobaSyn' : 'cobadefaultregime'
}
variables_to_report = {
'CobaSyn.I' : True
}
inspector = nineml_component_inspector()
inspector.inspect(nineml_component, timeHorizon = timeHorizon,
reportingInterval = reportingInterval,
parameters = parameters,
initial_conditions = initial_conditions,
active_regimes = active_regimes,
analog_ports_expressions = analog_ports_expressions,
event_ports_expressions = event_ports_expressions,
variables_to_report = variables_to_report)
results = inspector.showQtGUI()
return results, inspector
.format(outdir, texFile))
res = os.system(
'/usr/bin/pdflatex -interaction=nonstopmode -output-directory {0} {1}'
.format(outdir, texFile))
else:
res = os.system(
'/usr/bin/pdflatex -interaction=nonstopmode {0}'.format(texFile))
res = os.system(
'/usr/bin/pdflatex -interaction=nonstopmode {0}'.format(texFile))
return res
def showFile(pdf):
if os.name == 'nt':
os.filestart(pdf)
elif os.name == 'posix':
os.system('/usr/bin/xdg-open ' + pdf)
if __name__ == "__main__":
component = 'hierachical_iaf_1coba'
tex = component + '.tex'
pdf = component + '.pdf'
nineml_component = TestableComponent(component)()
inspector = nineml_component_inspector()
inspector.inspect(nineml_component)
createLatexReport(inspector, [], 'nineml-tex-template.tex', tex)
res = createPDF(tex)
showFile(pdf)
# Connect data reporter
simName = simulation.m.Name + strftime(" [%d.%m.%Y %H:%M:%S]", localtime())
if(datareporter.Connect("", simName) == False):
sys.exit()
# Initialize the simulation
simulation.Initialize(daesolver, datareporter, log)
# Solve at time=0 (initialization)
simulation.SolveInitial()
# Run
simulation.Run()
simulation.Finalize()
inspector = nineml_component_inspector()
inspector.inspect(nineml_comp)
tmpFolder = tempfile.gettempdir()
log_output = log.JoinMessages('\n')
plots = datareporter.createReportData(tmpFolder)
dictInputs = {}
dictInputs['parameters'] = parameters
dictInputs['initial_conditions'] = initial_conditions
dictInputs['analog_ports_expressions'] = analog_ports_expressions
dictInputs['event_ports_expressions'] = event_ports_expressions
dictInputs['active_regimes'] = active_regimes
dictInputs['variables_to_report'] = variables_to_report
dictInputs['timeHorizon'] = timeHorizon
dictInputs['reportingInterval'] = reportingInterval
