def simulate(pool, tstop=1000, vinit=-55):
    ''' simulation control 
    Parameters
    ----------
    cell: NEURON cell
        cell for simulation
    tstop: int (ms)
        simulation time
    vinit: int (mV)
        initialized voltage
    '''
    h.finitialize(vinit)
    for i in pool:
        cell = pc.gid2cell(i)
        balance(cell)
    if h.cvode.active():
        h.cvode.active()
    else:
        h.fcurrent()
    h.frecord_init()
    h.tstop = tstop
    h.v_init = vinit
    pc.set_maxstep(0.5)
    h.stdinit()
    pc.psolve(tstop)
Ejemplo n.º 2
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def simulate(pool, tstop=50000, vinit=-55):
    ''' simulation control
    Parameters
    ----------
    cell: NEURON cell
        cell for simulation
    tstop: int (ms)
        simulation time
    vinit: int (mV)
        initialized voltage
    '''
    h.finitialize(vinit)
    for i in pool:
        cell = pc.gid2cell(i)
        balance(cell)
    if h.cvode.active():
        h.cvode.active()
    else:
        h.fcurrent()
    h.frecord_init()
    h.tstop = tstop
    h.v_init = vinit
    pc.set_maxstep(0.5)
    h.stdinit()
    pc.psolve(tstop)
Ejemplo n.º 3
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def FiringOnset(leftI, rightI, precision, apc, stim, T, fr_set):
    import neuron
    from neuron import h
    from I_proc import stimulate
    while ((rightI - leftI) > precision * max([abs(rightI), abs(leftI)])):
        print("leftI is %f, rightI is %f" % (leftI, rightI))
        print("rightI-leftI: %f , precision: %f \n" %
              ((rightI - leftI), precision))
        h.finitialize()
        h.fcurrent()
        h.frecord_init()
        apc.n = 0
        mean = (leftI + rightI) / 2
        print('mean is %f' % (mean))
        h.stim = stimulate([0, stim, mean])
        h.tstop = T
        h.run()
        fr = apc.n / float(T / 1000)
        print('fr is %f' % (fr))
        if (fr <= fr_set):
            leftI = mean  # If the firing rate is too small, we will replace lowerbound with middle point
        else:
            rightI = mean  # If the firing rate is too large, we will replace upperbound with middle point

    if fr_set > 0:
        return rightI
    else:
        return leftI
Ejemplo n.º 4
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def go():
    h.dt = 0.1
    h.celsius = celsius
    h.finitialize(v_init)
    #neuron.init()

    # params:        RERE,        RETCa,        ***RETCb,     TCRE,        PYPY,       PYIN,       INPYa,                     ***INPYb,                  PYRE,        PYTC,        TCPY,        TCIN
    assign_synapses(RERE * 0.2, RETCa * 0.02, RETCb * 0.04, TCRE * 0.2,
                    PYPY * 0.6, PYIN * 0.2, INPYa * gabaapercent * 0.15,
                    INPYb * gababpercent * 0.03, PYRE * 1.2, PYTC * 0.01,
                    TCPY * 1.2, TCIN * 0.4)
    #assign_synapses(gRERE_GABAA, gRETC_GABAA,  gRETC_GABAB,  gTCRE_AMPA,  gPYPY_AMPA, gPYIN_AMPA, gINPY_GABAA,               gINPY_GABAB,               gPYRE_AMPA,  gPYTC_AMPA,  gTCPY_AMPA,  gTCIN_AMPA)

    h.fcurrent()
    h.cvode.re_init()
    h.frecord_init()

    printPYinfo(0)
    printINinfo(0)
    printTCinfo(0)
    printREinfo(0)
    printWeight(0)

    field.append(0)
    while h.t < tstop:
        h.fadvance()
        field.append(xfield(230, fielddist, watchneuron))
Ejemplo n.º 5
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def DetermineStdI(leftStd, rightStd, precision_std, apc, mean, stim, tau, dt,
                  T, fr_set, seednumber):
    import neuron
    from neuron import h
    from I_proc import stimulate
    while ((rightStd - leftStd) >
           precision_std * max([abs(rightStd), abs(leftStd)])):
        if leftStd == 0 and rightStd < 1e-7:
            break
            return rightStd
        print("leftStd is %f, rightStd is %f" % (leftStd, rightStd))
        print("rightStd-leftStd: %f , precision_std: %f \n" %
              ((rightStd - leftStd), precision_std))
        h.finitialize()
        h.fcurrent()
        h.frecord_init()
        apc.n = 0
        std = (leftStd + rightStd) / 2
        print('std for test is %f' % (std))
        h.stim = stimulate([1, stim, mean, std, tau, dt, T, seednumber])
        h.tstop = T
        h.run()
        fr = apc.n / float(T / 1000)
        print('fr is %f' % (fr))
        if (fr <= fr_set):
            leftStd = std
        else:
            rightStd = std

    return std
Ejemplo n.º 6
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 def initialise(self, vrest=-65):
     """
     Initialise the model, to launch before each simulations
     """
     for sec in h.allsec():
         h.finitialize(vrest, sec)
         h.fcurrent(sec)
     h.frecord_init()
Ejemplo n.º 7
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def simulation(model, tau, posNa, T, threshold, stim_mean, stim_std, frequency, dt=0.025, seednumber=1): 
  '''
  simulation(object) -> va (axonal voltage at the AP initiation site in mV)
  Simulate the neuron model based on model setup and stimulus parameters.
  
  Parameters: Meanings [Example Values]
  model: model name ['Brette']
  tau: correlation time of stimulus (ms) [5]
  posNa: position of sodium channels (um) [20]
  T: duration of stimulus and simulation (ms) [20000]
  threshold: axonal reset voltage for finishing spikes (mV) [-23]
  stim_mean: mean of stochastic stimulus (nA) [0.0185]
  stim_std: std of stochastic stimulus (nA) [0.046]
  dt: time step of model simulation (ms) [0.025]
  seednumber: random seed number for stimulus generation [1]
  '''
  import os, sys
  from neuron import h
  from math import pi
  import numpy as np

  # Load parameters into NEURON.
  h('dt=%f'%(dt)) 
  h('posNa=%f'%(posNa)) 
  h('threshold=%f'%(threshold))
  
  # Set up neuron model.
  h.load_file('nrngui.hoc') # Load nrngui.
  h.load_file('../Models/%s/Neuron.hoc'%(model)) # Load hoc file of neuron model.
  h('access soma')
  h('objref APgen, stimulus, stim, vAIS, vSoma')
  h('axon APgen = new NetCon(&v(posNa/axon_L), sodiumchan,threshold,0,0)') # Define action potential generation.
  h('axon {sodiumchan.loc(posNa/axon_L)}') # Insert sodium channels in axon.

  # Set up stimulus.
  h.stimulus = h.IClamp(0.5) # Stimulus is injected in the middle of soma.
  h.stimulus.dur = T # duration of simulus
  h.stim = h.Vector()
  sinwave = 0.01*np.sin(2*pi*frequency*np.arange(int(T/dt))*dt/1000.0) # NEW!! sinewave
  h.stim.from_python(sinwave) # Generate the stimulus with the OU process. # !!!
  h('stim.play(&stimulus.amp, dt)') 

  # Axonal voltage recording
  h.vAIS = h.Vector(int(T/dt)) 
  h.vSoma = h.Vector(int(T/dt))
  h('vAIS.record(&axon.v(posNa/axon_L))') # Axonal voltage is recorded at the position of sodium channels.
  h('vSoma.record(&soma.v(0.5))')
  h.tstop = T # duration of simulation

  # Initiate model simulation
  h.finitialize()
  h.frecord_init()
  h.run()

  va = h.vAIS.to_python() # Convert NEURON vector to numpy array.
  vs = h.vSoma.to_python()
  return va, vs
Ejemplo n.º 8
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def runsim():
    t0 = time.time()  # clock start time

    pc.set_maxstep(
        10)  # sets the default max solver step in ms (purposefully large)

    for elec in lelec:
        elec.setup()
        elec.LFPinit()

    h.finitialize(
    )  # initialize cells to -65 mV, after all the NetCon delays have been specified
    if pcID == 0:
        for tt in range(0, int(h.tstop), printdt):
            h.cvode.event(tt, prsimtime)  # print time callbacks

    h.fcurrent()
    h.frecord_init(
    )  # set state variables if they have been changed since h.finitialize
    pc.psolve(h.tstop)  # actual simulation - run the solver
    pc.barrier()

    # these calls aggregate data across procs/nodes
    pc.allreduce(dp_rec_L2, 1)
    pc.allreduce(
        dp_rec_L5,
        1)  # combine dp_rec on every node, 1=add contributions together
    for elec in lelec:
        elec.lfp_final()
    net.aggregate_currents(
    )  # aggregate the currents independently on each proc
    # combine net.current{} variables on each proc
    pc.allreduce(net.current['L5Pyr_soma'], 1)
    pc.allreduce(net.current['L2Pyr_soma'], 1)

    pc.barrier()

    # write time and calculated dipole to data file only if on the first proc
    # only execute this statement on one proc
    savedat(p, pcID, t_vec, dp_rec_L2, dp_rec_L5, net)

    for elec in lelec:
        print('end; t_vec.size()', t_vec.size(), 'elec.lfp_t.size()',
              elec.lfp_t.size())

    if pcID == 0:
        if debug: print("Simulation run time: %4.4f s" % (time.time() - t0))
        if debug: print("Simulation directory is: %s" % ddir.dsim)
        if paramrw.find_param(doutf['file_param'],
                              'save_spec_data') or usingOngoingInputs(
                                  doutf['file_param']):
            runanalysis(p, doutf['file_param'], doutf['file_dpl_norm'],
                        doutf['file_spec'])  # run spectral analysis
        if paramrw.find_param(doutf['file_param'], 'save_figs'):
            savefigs(ddir, p, p_exp)  # save output figures

    pc.barrier()  # make sure all done in case multiple trials
Ejemplo n.º 9
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def prun(runState):
    h.stdinit()
    if runState == 1:
        pnm.psolve(h.tstop / 2.)
        savestate()
    else:
        restorestate()
    h.frecord_init()
    pnm.psolve(h.tstop)
    pspike()
Ejemplo n.º 10
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def simulate(cell, tstop=400, vinit=-55):
    ''' simulation control
    Parameters
    ----------
    cell: NEURON cell
        cell for simulation
    tstop: int (ms)
        simulation time
    vinit: int (mV)
        initialized voltage
    '''
    h.finitialize(vinit)
    balance(cell)
    if h.cvode.active():
        h.cvode.active()
    else:
        h.fcurrent()
    h.frecord_init()
    h.tstop = tstop
    h.v_init = vinit
    h.run()
    if cell.numofmodel == 9 or cell.numofmodel == 10 or cell.numofmodel == 12:
        running_ = 1
        if cell.numofmodel == 9:
            dl = 0
            d_t = 60000
        elif cell.numofmodel == 10:
            dl = 1000
            d_t = 40
        else:
            dl = 800
            d_t = 10
        h.stdinit()
        for n in range(3):
            cell.x_application = cell.x_application + dl
            if n == 0:
                cell.dl = 5000
                cell.x_application = 0
                print(cell.x_application)
            else:
                cell.dl = 30050
                cell.x_application = -400
            cell.distance()
            for item in cell.diffs:
                item.tx1 = h.t + 5
                # item.initial = 0#item.atp
                # if n == 0:
                #     item.c0cleft = 0.01#item.c0cleft
                # else:
                item.c0cleft = item.c0cleft
                item.h = cell.distances.get(cell.diffusions.get(item))
            h.continuerun(h.t + d_t)
        h.continuerun(h.t + 500)
Ejemplo n.º 11
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    def reset(self):
        print("Simulation initialization.")
        h.initnrn()
        h.frecord_init()
        h.finitialize(self.init_v * mV)

        if self.init_sleep > 0:
            print("sleep before run for: %s seconds" % self.init_sleep)
            time.sleep(self.init_sleep)

        if self.warmup > 0:
            h.dt = self.warmup / 10
            h.continuerun(self.warmup * ms)
        h.dt = self.dt
Ejemplo n.º 12
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    def min_sim(self):
        """
        Launch a minimal simulation to test the model and determine its
        resting potential empirically
        """
        for sec in h.allsec():
            h.finitialize(-65, sec)
            h.fcurrent(sec)
        h.frecord_init()

        while h.t < 200:  # Launch a simulation
            h.fadvance()

        # Record the soma voltage after this minimal stimulation to find v_rest
        soma = getattr(h,   "soma")
        self.vrest = getattr(soma,   "v")
Ejemplo n.º 13
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    def min_sim(self, TSTOP=100):
        """
        Launch a minimal simulation to test the model and determine its resting potential empirically
        """
        vrec = h.Vector()
        vrec.record(self.soma(0.5)._ref_v)

        for sec in h.allsec():
            h.finitialize(-65, sec)
            h.fcurrent(sec)
        h.frecord_init()

        while h.t < TSTOP: #Launch a simulation
            h.fadvance()

        vrest = np.array(vrec)[-1]

        return vrest
Ejemplo n.º 14
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    def run(self, cell, cmd, temp=22, dt=0.025):
        """
        Run a single current-clamp recording on *section*.
        
        Parameters:
        cell : Cell
            The Cell instance to test. IClamp will be attached to 
            cell.soma(0.5).
        cmd : array
            Array of current command values
        temp : 
            temperature of simulation (22)
        dt : 
            timestep of simulation (0.025)
        """
        self.reset()
        self.cell = cell
        self.current_cmd = cmd
        self.dt = dt
        self.temp = temp

        tend = len(cmd) * dt

        # Configure IClamp
        istim = h.iStim(0.5, sec=cell.soma)
        istim.delay = 0
        istim.dur = 1e9  # these actually do not matter...
        istim.iMax = 0.0
        i_stim = h.Vector(cmd)
        i_stim.play(istim._ref_i, h.dt, 0)

        # Connect recording vectors
        self['vm'] = cell.soma(0.5)._ref_v
        self['i_inj'] = istim._ref_i
        self['time'] = h._ref_t

        # GO
        h.dt = dt
        h.celsius = temp
        h.tstop = tend
        cell.initialize()
        h.frecord_init()
        while h.t < h.tstop:
            h.fadvance()
Ejemplo n.º 15
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def simulate(cell, tstop=1500, vinit=-55):
    ''' simulation control 
    Parameters
    ----------
    cell: NEURON cell
        cell for simulation
    tstop: int (ms)
        simulation time
    vinit: int (mV)
        initialized voltage
    '''
    h.finitialize(vinit)
    balance(cell)
    if h.cvode.active():
        h.cvode.active()
    else:
        h.fcurrent()
    h.frecord_init()
    h.tstop = tstop
    h.v_init = vinit
    h.run()
Ejemplo n.º 16
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def simulate(cell, tstop=500, vinit=-60):
    ''' simulation control
    Parameters
    ----------
    cell: NEURON cell
        cell for simulation
    tstop: int (ms)
        simulation time
    vinit: int (mV)
        initialized voltage
    '''
    h.finitialize(vinit)
    balance(cell)
    if h.cvode.active():
        h.cvode.active()
    else:
        h.fcurrent()
    h.frecord_init()
    h.tstop = tstop
    h.v_init = vinit
    h.run()
Ejemplo n.º 17
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def run_neuron_simulator(warmup=2000,
                         dt_warmup=10,
                         dt_sim=0.1,
                         t_start=0,
                         t_stop=600,
                         v_init=-60):
    h.cvode.active(0)
    dt = 0.1
    h.steps_per_ms = 1.0 / dt
    h.finitialize(v_init)
    h.t = -warmup
    h.secondorder = 0
    h.dt = dt_warmup
    while h.t < -100:
        h.fadvance()

    h.secondorder = 2
    h.t = 0
    h.dt = dt_sim
    """Setup run control for -100 to 1500"""
    h.frecord_init()  # Necessary after changing t to restart the vectors
    while h.t < t_stop:
        h.fadvance()
Ejemplo n.º 18
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    """Initialization for -2000 to -100"""
    h.cvode.active(0)
    dt = 0.1
    h.steps_per_ms = 1.0 / dt
    h.finitialize(-60)
    h.t = -2000
    h.secondorder = 0
    h.dt = 10
    while h.t < -100:
        h.fadvance()

    h.secondorder = 2
    h.t = 0
    h.dt = 0.1
    """Setup run control for -100 to 1500"""
    h.frecord_init()  # Necessary after changing t to restart the vectors
    while h.t < 600:
        h.fadvance()
    print("Done Running")

    tuned_save_file_name = (str(nw) + "_data_paradigm_local-pattern" +
                            "-separation_run_scale_seed_" + str(run).zfill(3) +
                            '_' + str(input_scale).zfill(3) + '_' + str(seed))
    nw.shelve_network(savedir, tuned_save_file_name)

    fig = nw.plot_aps(time=600)
    tuned_fig_file_name = (str(nw) + "_spike-plot_paradigm_local-pattern" +
                           "-separation_run_scale_seed_" + str(run).zfill(3) +
                           '_' + str(input_scale).zfill(3) + '_' + str(seed))
    nw.save_ap_fig(fig, savedir, tuned_fig_file_name)
Ejemplo n.º 19
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def simulation(model,
               tau,
               posNa,
               T,
               stim_mean,
               stim_std,
               dt=0.025,
               seednumber=1,
               stim_type='OU',
               amplitude=[0],
               frequency=[0],
               electrode_place='soma'):
    '''

  simulation(object) -> va (axonal voltage at the AP initiation site in mV)

  Simulate the neuron model based on model setup and stimulus parameters.
  
  Parameters: Meanings [Example Values]
  model: model name ['GE_diam_0']
  tau: correlation time of stimulus (ms) [5]
  posNa: AP initiation site on axon (um) [47]
  T: duration of stimulus and simulation (ms) [20000]
  stim_mean: mean of stochastic stimulus (nA) [0.0]
  stim_std: std of stochastic stimulus (nA) [0.0346]
  dt: time step of model simulation (ms) [0.025]
  seednumber: random seed number for stimulus generation [1]
  stim_type: type of stimulus ['OU']
  amplitude: amplitude of the sinusoidal signal in unit of stim_std [0.1] 
  frequency: frequency of the sinusoidal signal added to background noise (Hz) [1, 2, 5, 10, 20, ..., 1000] 
  electrode_place: the place of the input stimulus ['soma']
  '''
    import os, sys
    from neuron import h

    # Load parameters into NEURON.
    h('dt=%f' % (dt))
    h('posNa=%f' % (posNa))

    # Set up neuron model.
    h.load_file('nrngui.hoc')  # Load nrngui.
    h('objref cell')  # create neuron model
    h.load_file('../Models/%s/%s.hoc' % (model, model))
    exec('h.cell = h.%s()' % (model))
    h.cell.create_model()
    h.cell.biophys()
    h('v_init = -90')  # initial voltage
    h('objref stimulus, stim, vAIS')
    if electrode_place == 'soma':
        h.stimulus = h.IClamp(0.5)
    else:
        h.stimulus = h.IClamp(h.cell.axon[0](0.94))
    h.stimulus.dur = T

    h.stim = h.Vector()
    h.stim.from_python(
        stimulate([
            stim_mean, stim_std, tau, dt, T, seednumber, stim_type, amplitude,
            frequency
        ]))  # Generate the stimulus with the OU process.
    h('stim.play(&stimulus.amp, dt)')
    h.finitialize()
    h.frecord_init()

    # Axonal voltage recording
    h.vAIS = h.Vector(int(T / dt))
    h.vAIS.record(
        h.cell.axon[0](h.posNa / h.cell.axon[0].L)._ref_v
    )  # Axonal voltage is recorded on the AIS with a distance of posNa. Total length of AIS is L.
    # h.vAIS.record(h.cell.soma[0](0.5)._ref_v)
    h.tstop = T  # duration of simulation

    # Initiate model simulation
    h.finitialize()
    h.frecord_init()
    h.run()

    va = h.vAIS.to_python()  # Convert NEURON vector to numpy array.
    return va
Ejemplo n.º 20
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for prs, post in np.genfromtxt("../se.ssv").astype(int):
    scons.append(h.NetCon(S[prs].s, E[post].cell))

sys.stderr.write("====== Network Created! =======\n")

for econ in econs:
    econ.weight[0], econ.delay = excw, excd
for icon in icons:
    icon.weight[0], icon.delay = inhw, inhd
for scon in scons:
    scon.weight[0], scon.delay = stmw, stmd

h.dt = 0.1
h.finitialize()
h.fcurrent()
h.frecord_init()

endbuild = time.time()

while h.t < 1000.:
    h.fadvance()

endsimulate = time.time()

print("Building time     : %.2f s" % (endbuild - startbuild))
print("Simulation time   : %.2f s" % (endsimulate - endbuild))
print("Time step         : %.2f ms" % (h.dt))

spkse = np.array([(x, ni) for ni, nE in enumerate(E)
                  for x in list(np.array(nE.spk))])
spksi = np.array([(x, ni + Ne + 100) for ni, nI in enumerate(I)
Ejemplo n.º 21
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def pyDentate(input_grid_out, seed_2, n_traj, dur_ms):
    savedir = os.getcwd()
    input_scale = 1000
    seed_3 = seed_2 + 150  #seed_3 for network generation & simulation
    # Where to search for nrnmech.dll file. Must be adjusted for your machine.
    # dll_files = [("C:\\Users\\DanielM\\Repos\\models_dentate\\"
    #               "dentate_gyrus_Santhakumar2005_and_Yim_patterns\\"
    #               "dentategyrusnet2005\\nrnmech.dll"),
    #              "C:\\Users\\daniel\\Repos\\nrnmech.dll",
    #              ("C:\\Users\\Holger\\danielm\\models_dentate\\"
    #               "dentate_gyrus_Santhakumar2005_and_Yim_patterns\\"
    #               "dentategyrusnet2005\\nrnmech.dll"),
    #              ("C:\\Users\\Daniel\\repos\\"
    #               "dentate_gyrus_Santhakumar2005_and_Yim_patterns\\"
    #               "dentategyrusnet2005\\nrnmech.dll"),
    #               ("/home/baris/Python/mechs_7-6_linux/"
    #                "x86_64/.libs/libnrnmech.so")]

    # for x in dll_files:
    #     if os.path.isfile(x):
    #         dll_dir = x
    # print("DLL loaded from: " + dll_dir)
    # h.nrn_load_dll(dll_dir)

    #number of cells
    n_grid = 200
    n_granule = 2000
    n_mossy = 60
    n_basket = 24
    n_hipp = 24

    np.random.seed(seed_3)  # seed_3 for connections in the network

    # Randomly choose target cells for the GridCell lines
    gauss_gc = stats.norm(loc=1000, scale=input_scale)
    gauss_bc = stats.norm(loc=12,
                          scale=(input_scale / float(n_granule)) * n_basket)
    pdf_gc = gauss_gc.pdf(np.arange(n_granule))
    pdf_gc = pdf_gc / pdf_gc.sum()
    pdf_bc = gauss_bc.pdf(np.arange(n_basket))
    pdf_bc = pdf_bc / pdf_bc.sum()
    GC_indices = np.arange(n_granule)
    start_idc = np.random.randint(0, n_granule - 1, size=n_grid)

    PP_to_GCs = []
    for x in start_idc:
        curr_idc = np.concatenate((GC_indices[x:n_granule], GC_indices[0:x]))
        PP_to_GCs.append(
            np.random.choice(curr_idc, size=100, replace=False, p=pdf_gc))

    PP_to_GCs = np.array(PP_to_GCs)

    BC_indices = np.arange(n_basket)
    start_idc = np.array(((start_idc / float(n_granule)) * 24), dtype=int)

    PP_to_BCs = []
    for x in start_idc:
        curr_idc = np.concatenate((BC_indices[x:24], BC_indices[0:x]))
        PP_to_BCs.append(
            np.random.choice(curr_idc, size=1, replace=False, p=pdf_bc))
    PP_to_BCs = np.array(PP_to_BCs)

    # generate temporal patterns out of grid cell act profiles as an input for pyDentate
    # input_grid_out = inhom_poiss(par_traj, n_traj, dt_s=0.0001, seed=seed_2)

    np.random.seed(seed_3)  #seed_3 again for network generation & simulation

    granule_output = np.empty((n_granule, n_traj), dtype=np.ndarray)
    mossy_output = np.empty((n_mossy, n_traj), dtype=np.ndarray)
    basket_output = np.empty((n_basket, n_traj), dtype=np.ndarray)
    hipp_output = np.empty((n_hipp, n_traj), dtype=np.ndarray)

    for trj in range(n_traj):
        nw = net_tunedrev.TunedNetwork(seed_3, input_grid_out[:, trj],
                                       PP_to_GCs, PP_to_BCs)
        # Attach voltage recordings to all cells
        nw.populations[0].voltage_recording(range(n_granule))
        nw.populations[1].voltage_recording(range(n_mossy))
        nw.populations[2].voltage_recording(range(n_basket))
        nw.populations[3].voltage_recording(range(n_hipp))
        # Run the model
        """Initialization for -2000 to -100"""
        h.cvode.active(0)
        dt = 0.1
        h.steps_per_ms = 1.0 / dt
        h.finitialize(-60)
        h.t = -2000
        h.secondorder = 0
        h.dt = 10
        while h.t < -100:
            h.fadvance()

        h.secondorder = 2
        h.t = 0
        h.dt = 0.1
        """Setup run control for -100 to 1500"""
        h.frecord_init()  # Necessary after changing t to restart the vectors
        while h.t < dur_ms:
            h.fadvance()
        print("Done Running")

        granule_output[:, trj] = np.array(
            [cell[0].as_numpy() for cell in nw.populations[0].ap_counters])
        # mossy_output[:,trj] =  np.array([cell[0].as_numpy() for cell in nw.populations[1].ap_counters])
        # basket_output[:,trj] =  np.array([cell[0].as_numpy() for cell in nw.populations[2].ap_counters])
        # hipp_output[:,trj] =  np.array([cell[0].as_numpy() for cell in nw.populations[3].ap_counters])

    return granule_output, mossy_output, basket_output, hipp_output
Ejemplo n.º 22
0
def simulate():
    h.frecord_init()
    h.tstop = tstop
    h.run()
Ejemplo n.º 23
0
def simulate(tau_facil,
             tau_rec,
             stim_freq,
             celltype,
             tau_1=0.3,
             tau_2=0.6,
             u0=0.078,
             sampling_interval=0.5,
             v_clamp=-70.42,
             sec='proxd'):
    """Simulates a frequency stimulation of the tmgexp2syn meachnism onto a
    neuron and measure the conductance at the soma.

    Parameters
    ----------
    tau_facil : numeric
        facilitation time constant of the tmgexp2syn mechanism
        
    tau_rec : numeric
        recovery time constant of the tmgexp2syn mechanism
        
    stim_freq : numeric
        stimulation frequency in Hz
        
    celltype : ouropy.GenNeuron
        A class that inherits from ouropy.GenNeuron
        
    tau_1 : numeric
        Synaptic rise time
        
    tau_2 : numeric
        Synaptic decay time
        
    u0 : float
        The u0 parameters as specified in tmgexp2syn
        
    sampling_interval : numeric
        The sampling interval in ms
        
    v_clamp : numeric
        Holding potential of the
        
    Returns
    -------
    peaks_norm : ndarray
        Peak conductances normalized to first peak
    
    garr_norm : ndarray
        Conductance array normalized to first peak
    """
    # Resolve simulation hyperparameters
    left_pad, right_pad = 50, 100  # in ms
    simdur = left_pad + right_pad + 10 * (1000 / stim_freq)
    # Create cell
    mycell = celltype()
    # Create synapse
    syn = h.tmgexp2syn(mycell.get_segs_by_name(sec)[0](0.5))
    syn.tau_1 = tau_1
    syn.tau_2 = tau_2
    syn.tau_facil = tau_facil
    syn.tau_rec = tau_rec
    syn.u0 = u0
    syn.e = 0
    # Create stimulation
    stim_period_ms = 1000 / stim_freq
    stim = h.NetStim()
    stim.interval = stim_period_ms
    stim.start = left_pad
    stim.number = 10
    nc = h.NetCon(stim, syn)
    nc.weight[0] = 0.001
    # Create voltage clamp
    c = h.SEClamp(mycell.soma(0.5))
    c.dur1 = simdur
    c.amp1 = v_clamp
    c.rs = 0.1
    # Create recording vector
    ivec = h.Vector()
    ivec.record(c._ref_i)
    # Start simulation
    sample_period_ms = sampling_interval
    h.cvode.active(0)
    h.finitialize(-70.42)
    h.t = -2000
    h.secondorder = 0
    h.dt = 10
    while h.t < -100:
        h.fadvance()
    h.secondorder = 0
    h.t = 0
    h.dt = sample_period_ms
    h.steps_per_ms = 1.0 / h.dt
    h.frecord_init()  # Necessary after changing t to restart the vectors
    while h.t < simdur:
        h.fadvance()
    # Get Peaks from output

    iarr = np.array(ivec)
    garr = (iarr - iarr[0:50].mean()) / v_clamp
    stim_dtp = int(np.around(stim.interval / sampling_interval))
    pad_dtp = int(left_pad / sampling_interval)
    t_stim = np.arange(pad_dtp, stim_dtp * 11 + pad_dtp, stim_dtp)
    #dtp_stim = np.array(t_stim / sampling_interval, dtype=np.int)
    dtp_stim = np.array(t_stim, dtype=np.int)
    gvec_split = np.array(np.split(garr, dtp_stim)[1:-1])

    peaks = gvec_split.max(axis=1)
    peaks_norm = peaks / peaks[0]
    garr_norm = garr / peaks[0]

    return peaks_norm, garr_norm
Ejemplo n.º 24
0
def _simulate_single_trial(net):
    """Simulate one trial."""
    from .parallel import rank, nhosts, pc, cvode
    from neuron import h
    h.load_file("stdrun.hoc")

    # Now let's simulate the dipole
    if rank == 0:
        print("running on %d cores" % nhosts)

    # global variables, should be node-independent
    h("dp_total_L2 = 0.")
    h("dp_total_L5 = 0.")

    # Set tstop before instantiating any classes
    h.tstop = net.params['tstop']
    h.dt = net.params['dt']  # simulation duration and time-step
    h.celsius = net.params['celsius']  # 37.0 - set temperature

    # We define the arrays (Vector in numpy) for recording the signals
    t_vec = h.Vector()
    t_vec.record(h._ref_t)  # time recording
    dp_rec_L2 = h.Vector()
    dp_rec_L2.record(h._ref_dp_total_L2)  # L2 dipole recording
    dp_rec_L5 = h.Vector()
    dp_rec_L5.record(h._ref_dp_total_L5)  # L5 dipole recording

    net.move_cells_to_pos()  # position cells in 2D grid

    # sets the default max solver step in ms (purposefully large)
    pc.set_maxstep(10)

    # initialize cells to -65 mV, after all the NetCon
    # delays have been specified
    h.finitialize()

    def prsimtime():
        print('Simulation time: {0} ms...'.format(round(h.t, 2)))

    printdt = 10
    if rank == 0:
        for tt in range(0, int(h.tstop), printdt):
            cvode.event(tt, prsimtime)  # print time callbacks

    h.fcurrent()
    # set state variables if they have been changed since h.finitialize
    h.frecord_init()
    # actual simulation - run the solver
    pc.psolve(h.tstop)

    pc.barrier()

    # these calls aggregate data across procs/nodes
    pc.allreduce(dp_rec_L2, 1)
    # combine dp_rec on every node, 1=add contributions together
    pc.allreduce(dp_rec_L5, 1)
    # aggregate the currents independently on each proc
    net.aggregate_currents()
    # combine net.current{} variables on each proc
    pc.allreduce(net.current['L5Pyr_soma'], 1)
    pc.allreduce(net.current['L2Pyr_soma'], 1)

    pc.barrier()  # get all nodes to this place before continuing

    dpl_data = np.c_[np.array(dp_rec_L2.to_python()) +
                     np.array(dp_rec_L5.to_python()),
                     np.array(dp_rec_L2.to_python()),
                     np.array(dp_rec_L5.to_python())]

    pc.gid_clear()
    pc.done()
    dpl = Dipole(np.array(t_vec.to_python()), dpl_data)
    if rank == 0:
        if net.params['save_dpl']:
            dpl.write('rawdpl.txt')

        dpl.baseline_renormalize(net.params)
        dpl.convert_fAm_to_nAm()
        dpl.scale(net.params['dipole_scalefctr'])
        dpl.smooth(net.params['dipole_smooth_win'] / h.dt)
    return dpl, net.spiketimes.to_python(), net.spikegids.to_python()
Ejemplo n.º 25
0
    def __call__(self,  input_spikes, bin_size=10, el=1):
        """
        Launch a simulation of a given time with a binary event happening
        or not in each time bin

        Parameters
        ----------
        input_spikes: 2-D numpy array of Bool
            contain the occurence or not of an event. Each line is a set of
            signals
            and each column corresponds to a time bin
        bin_size: float
            the size of a time bin in ms.
        el: float
            elementary weight,   it will scale all the weights

        Comments
        --------
        It seems that when multiple go method are done it does not
        change the output vector.
        """
        # Set the time to 0
        h.t = 0
        try:
            weights = self.weights*el
            where_what = self.input_locations
            assert len(self.weights) == len(self.input_locations)
        except AttributeError:
            return "Weights or the input_locations not set. Simulation aborted"
        except AssertionError:
            print("Weights or the input_locations not match. Set default w")
            self.weights = np.ones(len(self.input_locations))

        # Test if signal and stimulation match.
        try:
            assert len(input_spikes) == len(self.input_locations)
        except AssertionError:
            print(self.where_what)
            print(input_spikes)
            print("Number of input neuron does not match number of synapses")
            print("Aborting simulation")
            return

        # Set the input spike time
        self.tstims = bin2time(input_spikes,   bin_size)
        self.TSTOP = bin_size * input_spikes.shape[1]
        tstims = self.tstims

        # This is to prevent remanescence of the synapse
        # Otherwise you can become crazy!!
        if len(self.syn) >= 1:
            for key in self.syn.keys():
                del self.syn[key]

        # Set the inputs
        for i,   tstim in enumerate(tstims):
            self.add_stim(where_what[i],
                          name='Stream'+str(i),
                          tstim=tstim,
                          w=weights[i])

        # Set the initial membrane potential
        if not hasattr(self,  'vrest'):
            self.min_sim()

        # Record Time
        record_time = h.Vector()
        record_time.record(h._ref_t)

        # Record Voltage
        self.record_v()

        # Set the time at zero
        h.t = 0
        # ReInitialise the sections
        for sec in h.allsec():
            h.finitialize(self.vrest,   sec)
            h.fcurrent(sec)
        h.frecord_init()

        # Launch a simulation with or without adding spikes
        if self.spike:
            # Need to hasck the recording of the data
            self.data['soma'] = [[]]
            self.data['soma'][0].append(h.soma.v)
            refrac_abs = 200
            threshold = -40
            spk = False
            refrac = 0
            h.t = 0
            while h.t < self.TSTOP:
                h.fadvance()
                # Spike if voltage cross threshold and no refractoriness
                if h.soma.v >= threshold and not refrac:
                    h.soma.v = 20
                    spk = True

                # If the neuron spiked add one to the refractory period
                if spk:
                    refrac += 1

                # Put the soma back to a reset voltage
                if refrac == 2:
                    h.soma.v = threshold - 10

                # Reset the absolute refrac period
                if refrac >= refrac_abs:
                    refrac = 0
                    spk = False

                self.data['soma'][0].append(h.soma.v)

        else:
            while h.t < self.TSTOP:
                h.fadvance()

        # Copy time into a vector
        self.rec_t = np.array(record_time)