IT2 validation

Author: HengyeZhu

NeuroML2/compare_MC/IT2/IT2_json.py

@@ -1,9 +1,20 @@
+import os
+# Force headless plotting for Matplotlib (as in RE_netpy)
+os.environ["MPLBACKEND"] = "Agg"
+import matplotlib
+matplotlib.use("Agg")
+# Ensure NEURON runs headless in non-GUI environments
+os.environ["NEURON_NO_GUI"] = "1"
+os.environ.pop("DISPLAY", None)
+print(f"[IT2_netpy] Headless env: DISPLAY={os.environ.get('DISPLAY')}, NEURON_NO_GUI={os.environ.get('NEURON_NO_GUI')}, MPLBACKEND={os.environ.get('MPLBACKEND')}")
+
 from netpyne import specs, sim
 import pprint
 
-netParams = specs.NetParams() 
-## IT2 cell properties
-soma = {'geom': {}, 'ions': {}, 'mechs': {}, 'vinit': -85.7, 'threshold': 5.0} 
+netParams = specs.NetParams()
+
+## IT2 cell properties (NetPyNE version using same mechanisms as IT2_reduced_cell.nml)
+soma = {'geom': {}, 'ions': {}, 'mechs': {}, 'vinit': -85.7, 'threshold': 5.0}
 soma['geom'] = {'diam': 28.2149102762, 'L': 48.4123467666, 'Ra': 70.0015514222, 'cm': 2.4998269977, 'nseg': 1, 'pt3d': []}
 soma['geom']['pt3d'].append((0, 0, 0, 28.2149102762))
 soma['geom']['pt3d'].append((0, 48.4123467666, 0, 28.2149102762))
@@ -144,28 +155,27 @@
 
 netParams.popParams['IT2'] = {'cellType': 'IT2_HH_reduced', 'numCells': 1}
 
-netParams.stimSourceParams['Input'] = {'type': 'IClamp', 'dur': 1600, 'del': 200, 'amp': 0.3}
+netParams.stimSourceParams['Input'] = {'type': 'IClamp', 'dur': 300, 'del': 200, 'amp': 0.3}
 netParams.stimTargetParams['Input->IT2'] = {'source': 'Input', 'sec': 'soma', 'loc': 0.5, 'conds': {'cellType': 'IT2_HH_reduced'}}
 netParams.defaultThreshold = 5.0
 # Simulation options
 simConfig = specs.SimConfig()       # object of class SimConfig to store simulation configuration
 
 simConfig.recordCells = ['all']
 simConfig.hParams['celsius'] = 34
-simConfig.duration = 2000           # Duration of the simulation, in ms
-simConfig.dt = 0.01       
-          # Internal integration timestep to use
+simConfig.duration = 700            # Duration of the simulation, in ms
+simConfig.dt = 0.025                # Internal integration timestep to use
 simConfig.verbose = False           # Show detailed messages
-simConfig.recordTraces = {'V_soma':{'sec':'soma','loc':0.5,'var':'v'}}  # Dict with traces to record
-simConfig.recordStep = 0.01            # Step size in ms to save data (eg. V traces, LFP, etc)
-simConfig.filename = 'IT2_reduced_all'         # Set file output name
-simConfig.savePickle = False        # Save params, network and sim output to pickle file
-simConfig.saveDataInclude = ['simData']  
-simConfig.saveJson = True 
-simConfig.analysis['plotTraces'] = {'include': [0], 'saveFig': True}  # Plot recorded traces for this list of cells
-simConfig.analysis['plotRaster'] = {'saveFig': True}                  # Plot a raster
+simConfig.recordTraces = {'V_soma': {'sec': 'soma', 'loc': 0.5, 'var': 'v'}}
+simConfig.recordStep = 0.025        # Step size in ms to save data
+simConfig.filename = 'IT2_reduced_all'
+simConfig.savePickle = False
+simConfig.saveDataInclude = ['simData']
+simConfig.saveJson = True
+# Disable built-in plotting during headless runs
+simConfig.analysis = {}
 
 # Create network and run simulation
 sim.createSimulateAnalyze(netParams = netParams, simConfig = simConfig)
 
-#import pylab; pylab.show()  # this line is only necessary in certain systems where figures appear empty
+#import pylab; pylab.show()  # this line is only necessary in certain systems where figures appear empty