project.generatedNetworkConnections.addSynapticConnection('aEPSP_Vervaeke_pf', 0, 0, 0, 0.5, 0, stim_seg_detailed, 0.5, 0, None) # delete all existing probes project.generatedPlotSaves.reset() # set up voltage recording at the specified points along the dendrite being stimulated project.generatedPlotSaves.addPlotSaveDetails('Golgi_reduced_v', project.simPlotInfo.getSimPlot('Golgi_reduced_v'), ArrayList([0]), ArrayList(rec_segs_reduced), False, False) project.generatedPlotSaves.addPlotSaveDetails('Golgi_detailed_v', project.simPlotInfo.getSimPlot('Golgi_detailed_v'), ArrayList([0]), ArrayList(rec_segs_detailed), False, False) # generate and compile neuron files print "Generating NEURON scripts..." simulator_seed = random.getrandbits(32) project.neuronFileManager.generateTheNeuronFiles(sim_config, None, NeuronFileManager.RUN_HOC,simulator_seed) compile_process = ProcessManager(project.neuronFileManager.getMainHocFile()) compile_success = compile_process.compileFileWithNeuron(0,0) # simulate if compile_success: print "Simulating: simulation reference " + sim_ref pm.doRunNeuron(sim_config) timefile_path = sim_path + '/time.dat' while not os.path.exists(timefile_path): time.sleep(0.1) data_string = "Data reference " + sim_ref for k,i in enumerate(rec_segs_detailed): data_string = data_string + " " + str(i) + " " + str(rec_dists_detailed[k]) print data_string System.exit(0)