Rxd parameter issue

[ddelpiano]

Use tutorial 3a and then changed RxD as per screenshot

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KeyError                                  Traceback (most recent call last)
~/git/netpyne-ui/netpyne_ui/netpyne_geppetto.py in instantiateNetPyNEModelInGeppetto(self=<netpyne_ui.netpyne_geppetto.NetPyNEGeppetto object>, args={})
    193             with redirect_stdout(sys.__stdout__):
    194                 if not args.get("usePrevInst", False):
--> 195                     netpyne_model = self.instantiateNetPyNEModel()
        netpyne_model = undefined
        self.instantiateNetPyNEModel = <bound method NetPyNEGeppetto.instantiateNetPyNEModel of <netpyne_ui.netpyne_geppetto.NetPyNEGeppetto object at 0x7f8a28195250>>
    196                     self.geppetto_model = self.model_interpreter.getGeppettoModel(netpyne_model)
    197 

~/git/netpyne-ui/netpyne_ui/netpyne_geppetto.py in instantiateNetPyNEModel(self=<netpyne_ui.netpyne_geppetto.NetPyNEGeppetto object>)
    665             #netcoded = jsonpickle.encode(self.netParams, unpicklable=False)
    666             #simcoded = jsonpickle.encode(self.simConfig, unpicklable=False)
--> 667             sim.create(self.netParams, self.simConfig)
        global sim.create = <function create at 0x7f8a290a3b90>
        self.netParams = <netpyne.specs.netParams.NetParams object at 0x7f89c3d4be50>
        self.simConfig = <netpyne.specs.simConfig.SimConfig object at 0x7f89c250ff10>
    668             sim.net.defineCellShapes()  # creates 3d pt for cells with stylized geometries
    669             sim.gatherData(gatherLFP=False)

~/git/netpyne-ui/src/netpyne/netpyne/sim/wrappers.py in create(netParams=<netpyne.specs.netParams.NetParams object>, simConfig=<netpyne.specs.simConfig.SimConfig object>, output=False, clearAll=False)
     55     conns = sim.net.connectCells()                # create connections between cells based on params
     56     stims = sim.net.addStims()                    # add external stimulation to cells (IClamps etc)
---> 57     rxd = sim.net.addRxD()                    # add reaction-diffusion (RxD)
        rxd = undefined
        sim.net.addRxD = <bound method addRxD of <netpyne.network.network.Network object at 0x7f89d05a4050>>
     58     simData = sim.setupRecording()             # setup variables to record for each cell (spikes, V traces, etc)
     59 

~/git/netpyne-ui/src/netpyne/netpyne/network/netrxd.py in addRxD(self=<netpyne.network.network.Network object>, nthreads=None)
     75         rxdParams = sim.net.params.rxdParams
     76         if 'regions' in rxdParams:
---> 77             self._addRegions(rxdParams['regions'])
        self._addRegions = <bound method _addRegions of <netpyne.network.network.Network object at 0x7f89d05a4050>>
        rxdParams = {constants: {ip3_init: 0.0, caDiff: 0.08, ip3Diff: 1.41, caci_init: 1e-05, caco_init: 2.0, gip3r: 1204000, gserca: 0.3913, gleak: 6.02, kserca: 0.1, kip3: 0.15, kact: 0.4, ip3rtau: 2000, fc: 0.8, fe: 0.2, margin: 20}, regions: {cyt: {'cells': ['I', 'E'], 'secs': ['Bdend', 'Adend3'], 'nrn_region': 'i', 'geometry': 'membrane', 'dimension': None, 'dx': None}, er: {'cells': 'all', 'secs': 'all', 'geometry': {'class': 'FractionalVolume', 'args': {'volume_fraction': 0.2}}}, cyt_er_membrane: {'cells': 'all', 'secs': 'all', 'geometry': {'class': 'ScalableBorder', 'args': {'scale': 1, 'on_cell_surface': False}}}, ecs: {'extracellular': True, 'xlo': -20, 'ylo': -520, 'zlo': -20, 'xhi': 120, 'yhi': 20, 'zhi': 120, 'dx': 5, 'volume_fraction': 0.2, 'tortuosity': 1.6}}, species: {ca: {'regions': ['cyt', 'er', 'ecs'], 'd': 0.08, 'charge': 2, 'initial': 'caco_init if isinstance(node,rxd.node.NodeExtracellular) else (0.0017 - caci_init * fc) / fe if node.region == er else caci_init'}, ip3: {'regions': ['cyt'], 'd': 1.41, 'initial': 0.0}}, states: {ip3r_gate_state: {'regions': ['cyt_er_membrane'], 'initial': 0.8}}, multicompartmentReactions: {serca: {'reactant': 'ca[cyt]', 'product': 'ca[er]', 'rate_f': 'gserca / ((kserca / (1000. * ca[cyt])) ** 2 + 1)', 'membrane': 'cyt_er_membrane', 'custom_dynamics': True}, leak: {'reactant': 'ca[er]', 'product': 'ca[cyt]', 'rate_f': 6.02, 'rate_b': 6.02, 'membrane': 'cyt_er_membrane'}, ip3r: {'reactant': 'ca[er]', 'product': 'ca[cyt]', 'rate_f': 'gip3r * (ip3[cyt] * 1000. * ca[cyt] / (ip3[cyt] + kip3) / (1000. * ca[cyt] + kact) * ip3r_gate_state[cyt_er_membrane]) ** 3', 'rate_b': 'gip3r * (ip3[cyt] * 1000. * ca[cyt] / (ip3[cyt] + kip3) / (1000. * ca[cyt] + kact) * ip3r_gate_state[cyt_er_membrane]) ** 3', 'membrane': 'cyt_er_membrane'}}, rates: {ip3rg: {'species': 'ip3r_gate_state[cyt_er_membrane]', 'rate': '(1. / (1 + 1000. * ca[cyt] / (0.3)) - ip3r_gate_state[cyt_er_membrane]) / ip3rtau'}}}
     78         if 'extracellular' in rxdParams:
     79             #self._addExtracellular(rxdParams['extracellular'])

~/git/netpyne-ui/src/netpyne/netpyne/network/netrxd.py in _addRegions(self=<netpyne.network.network.Network object>, params={cyt: {'cells': ['I', 'E'], 'secs': ['Bdend', 'A...': 5, 'volume_fraction': 0.2, 'tortuosity': 1.6}})
    159             nrnSecs = list(sim.h.allsec())
    160         else:
--> 161             cells = sim.getCellsList(param['cells'])
        cells = undefined
        sim.getCellsList = <function getCellsList at 0x7f89c51f4170>
        param = {'cells': ['I', 'E'], 'secs': ['Bdend', 'Adend3'], 'nrn_region': 'i', 'geometry': 'membrane', 'dimension': None, 'dx': None}
    162             nrnSecs = []
    163             for cell in cells:

~/git/netpyne-ui/src/netpyne/netpyne/sim/utils.py in getCellsList(include=['I', 'E'], returnGids=False)
     96 
     97         elif isinstance(condition, basestring):  # entire pop
---> 98             cellGids.extend(list(sim.net.pops[condition].cellGids))
        global cellGids.extend = undefined
        global list = undefined
        sim.net.pops = {E2: <netpyne.network.pop.Pop object at 0x7f89c231a790>, I2: <netpyne.network.pop.Pop object at 0x7f8a28fe6b10>, E4: <netpyne.network.pop.Pop object at 0x7f89c23cff50>, I4: <netpyne.network.pop.Pop object at 0x7f89c23cf690>, E5: <netpyne.network.pop.Pop object at 0x7f89c23cf790>, I5: <netpyne.network.pop.Pop object at 0x7f89c23eb250>}
        global condition.cellGids = undefined
     99 
    100         elif isinstance(condition, tuple) or isinstance(condition, list):  # subset of a pop with relative indices

~/git/netpyne-ui/src/netpyne/netpyne/specs/dicts.py in __getitem__(self={E2: <netpyne.network.pop.Pop object at 0x7f89c2...etpyne.network.pop.Pop object at 0x7f89c23eb250>}, k='I')
    195 
    196     def __getitem__(self, k):
--> 197         return super(ODict, self).__getitem__(k)
        global super = <class 'super'>
        global ODict = <class 'netpyne.specs.dicts.ODict'>
        self.__getitem__ = <bound method ODict.__getitem__ of {E2: <netpyne.network.pop.Pop object at 0x7f89c231a790>, I2: <netpyne.network.pop.Pop object at 0x7f8a28fe6b10>, E4: <netpyne.network.pop.Pop object at 0x7f89c23cff50>, I4: <netpyne.network.pop.Pop object at 0x7f89c23cf690>, E5: <netpyne.network.pop.Pop object at 0x7f89c23cf790>, I5: <netpyne.network.pop.Pop object at 0x7f89c23eb250>}>
        k = 'I'
    198 
    199 

KeyError: 'I'