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