Python Simulation.dump_data方法代码示例

# 需要导入模块: from simulation import Simulation [as 别名]
# 或者: from simulation.Simulation import dump_data [as 别名]
    def test_single_cell(cls):
        """Simulates a single deep LTS cell and plots the Vm and [Ca2+]"""
        config.LOGGER.info("/**************************************************************************")
        config.LOGGER.info(" *")
        config.LOGGER.info(" * Simulating a single cell: %s" % (cls.__name__))
        config.LOGGER.info(" *")
        config.LOGGER.info(" **************************************************************************/")
        sim = Simulation(cls.__name__)
        mycell = DeepLTS(DeepLTS.prototype, sim.model.path + "/DeepLTS")

        config.LOGGER.debug(("Created cell: %s" % mycell.path))
        vm_table = mycell.comp[mycell.presyn].insertRecorder("Vm_deepLTS", "Vm", sim.data)
        pulsegen = mycell.soma.insertPulseGen(
            "pulsegen", sim.model, firstLevel=3e-10, firstDelay=100e-3, firstWidth=200e-3
        )
        sim.schedule()
        if mycell.has_cycle():
            config.LOGGER.warning("WARNING!! CYCLE PRESENT IN CICRUIT.")
        sim.run(0.5)
        sim.dump_data("data")
        mycell.dump_cell("deepLTS.txt")
        if config.has_pylab:
            mus_vm = config.pylab.array(vm_table) * 1e3
            mus_t = linspace(0, sim.simtime * 1e3, len(mus_vm))
            try:
                nrn_vm = config.pylab.loadtxt("../nrn/mydata/Vm_deepLTS.plot")
                nrn_t = nrn_vm[:, 0]
                nrn_vm = nrn_vm[:, 1]
                config.pylab.plot(nrn_t, nrn_vm, "y-", label="nrn vm")
            except IOError:
                print "NEURON Data not available."
            config.pylab.plot(mus_t, mus_vm, "g-.", label="mus vm")
            config.pylab.legend()
            config.pylab.title("DeepLTS")
            config.pylab.show()

# 需要导入模块: from simulation import Simulation [as 别名]
# 或者: from simulation.Simulation import dump_data [as 别名]
    def test_single_cell(cls):
        """Simulates a single deep basket cell and plots the Vm and [Ca2+]"""
        config.LOGGER.info("/**************************************************************************")
        config.LOGGER.info(" *")
        config.LOGGER.info(" * Simulating a single cell: %s" % (cls.__name__))
        config.LOGGER.info(" *")
        config.LOGGER.info(" **************************************************************************/")
        sim = Simulation(cls.__name__)
        mycell = DeepBasket(DeepBasket.prototype, sim.model.path + "/DeepBasket")
        print "Created cell:", mycell.path
        vm_table = mycell.comp[mycell.presyn].insertRecorder("Vm_deepbask", "Vm", sim.data)
        ca_conc_path = mycell.soma.path + "/CaPool"
        ca_table = None
        if config.context.exists(ca_conc_path):
            ca_conc = moose.CaConc(ca_conc_path)
            ca_table = moose.Table("Ca_deepbask", sim.data)
            ca_table.stepMode = 3
            ca_conc.connect("Ca", ca_table, "inputRequest")
        kc_path = mycell.soma.path + "/KC"
        gk_table = None
        if config.context.exists(kc_path):
            gk_table = moose.Table("gkc", sim.data)
            gk_table.stepMode = 3
            kc = moose.HHChannel(kc_path)
            kc.connect("Gk", gk_table, "inputRequest")
            pymoose.showmsg(ca_conc)
        pulsegen = mycell.soma.insertPulseGen(
            "pulsegen", sim.model, firstLevel=3e-10, firstDelay=100e-3, firstWidth=200e-3
        )
        #         pulsegen1 = mycell.soma.insertPulseGen('pulsegen1', sim.model, firstLevel=3e-7, firstDelay=150e-3, firstWidth=10e-3)

        sim.schedule()
        if mycell.has_cycle():
            print "WARNING!! CYCLE PRESENT IN CICRUIT."
        t1 = datetime.now()
        sim.run(500e-3)
        t2 = datetime.now()
        delta = t2 - t1
        print "simulation time: ", delta.seconds + 1e-6 * delta.microseconds
        sim.dump_data("data")
        mycell.dump_cell("deepbask.txt")
        if config.has_pylab:
            mus_vm = config.pylab.array(vm_table) * 1e3
            nrn_vm = config.pylab.loadtxt("../nrn/mydata/Vm_deepbask.plot")
            nrn_t = nrn_vm[:, 0]
            mus_t = linspace(0, nrn_t[-1], len(mus_vm))
            nrn_vm = nrn_vm[:, 1]
            nrn_ca = config.pylab.loadtxt("../nrn/mydata/Ca_deepbask.plot")
            nrn_ca = nrn_ca[:, 1]
            config.pylab.plot(nrn_t, nrn_vm, "y-", label="nrn vm")
            config.pylab.plot(mus_t, mus_vm, "g-.", label="mus vm")
            #         if ca_table:
            #             ca_array = config.pylab.array(ca_table)
            #             config.pylab.plot(nrn_t, -nrn_ca, 'r-', label='nrn (-)ca')
            #             config.pylab.plot(mus_t, -ca_array, 'b-.', label='mus (-)ca')
            #             print config.pylab.amax(ca_table)
            config.pylab.legend()
            config.pylab.title("DeepBasket")
            config.pylab.show()

# 需要导入模块: from simulation import Simulation [as 别名]
# 或者: from simulation.Simulation import dump_data [as 别名]
    def test_single_cell(cls):
        """Simulates a single thalamocortical relay cell
        and plots the Vm and [Ca2+]"""

        config.LOGGER.info("/**************************************************************************")
        config.LOGGER.info(" *")
        config.LOGGER.info(" * Simulating a single cell: %s" % (cls.__name__))
        config.LOGGER.info(" *")
        config.LOGGER.info(" **************************************************************************/")
        sim = Simulation(cls.__name__)
        mycell = TuftedRS(TuftedRS.prototype, sim.model.path + "/TuftedRS")
        print 'MOOSE: Created cell:', mycell.path
        vm_table = mycell.comp[cls.presyn].insertRecorder('Vm_tuftRS', 'Vm', sim.data)
        # ca_conc_path = mycell.soma.path + '/CaPool'
        # ca_table = None
        # if config.context.exists(ca_conc_path):
        #     ca_conc = moose.CaConc(ca_conc_path)
        #     ca_table = moose.Table('Ca_tuftRS', sim.data)
        #     ca_table.stepMode = 3
        #     ca_conc.connect('Ca', ca_table, 'inputRequest')
        # kc_path = mycell.soma.path + '/KC'
        # gk_table = None
        # if config.context.exists(kc_path):
        #     gk_table = moose.Table('gkc', sim.data)
        #     gk_table.stepMode = 3
        #     kc = moose.HHChannel(kc_path)
        #     kc.connect('Gk', gk_table, 'inputRequest')
        #     pymoose.showmsg(ca_conc)
        pulsegen = mycell.soma.insertPulseGen('pulsegen', sim.model, firstLevel=1e-9, firstDelay=100e-3, firstWidth=200e-3)
#         pulsegen1 = mycell.soma.insertPulseGen('pulsegen1', sim.model, firstLevel=3e-7, firstDelay=150e-3, firstWidth=10e-3)
        sim.schedule()
        if mycell.has_cycle():
            print "WARNING!! CYCLE PRESENT IN CICRUIT."
        t1 = datetime.now()
        sim.run(500e-3)
        t2 = datetime.now()
        delta = t2 - t1
        print 'MOOSE: simulation time: ', delta.seconds + 1e-6 * delta.microseconds
        sim.dump_data('data')
        # mycell.dump_cell('tuftRS.txt')
        if config.has_pylab:
            mus_vm = config.pylab.array(vm_table) * 1e3
            nrn_vm = config.pylab.loadtxt('../nrn/mydata/Vm_tuftRS.plot')
            nrn_t = nrn_vm[:, 0]
            mus_t = linspace(0, nrn_t[-1], len(mus_vm))
            nrn_vm = nrn_vm[:, 1]
            # nrn_ca = config.pylab.loadtxt('../nrn/mydata/Ca_tuftRS.plot')
            # nrn_ca = nrn_ca[:,1]
            config.pylab.plot(nrn_t, nrn_vm, 'y-', label='nrn vm')
            config.pylab.plot(mus_t, mus_vm, 'g-.', label='mus vm')
    #         if ca_table:
    #             ca_array = config.pylab.array(ca_table)
    #             config.pylab.plot(nrn_t, -nrn_ca, 'r-', label='nrn (-)ca')
    #             config.pylab.plot(mus_t, -ca_array, 'b-.', label='mus (-)ca')
    #             print config.pylab.amax(ca_table)
            config.pylab.legend()
            config.pylab.title('tuftedRS')
            config.pylab.show()

# 需要导入模块: from simulation import Simulation [as 别名]
# 或者: from simulation.Simulation import dump_data [as 别名]
    def test_single_cell(cls):
        """Simulates a single spiny stellate cell and plots the Vm and
        [Ca2+]"""

        config.LOGGER.info("/**************************************************************************")
        config.LOGGER.info(" *")
        config.LOGGER.info(" * Simulating a single cell: %s" % (cls.__name__))
        config.LOGGER.info(" *")
        config.LOGGER.info(" **************************************************************************/")
        sim = Simulation(cls.__name__)
        proto = TraubCell.read_proto("SpinyStellate.p", "SpinyStellate_1", SpinyStellate.chan_params)
        print 'Model path', sim.model.path , 'proto', proto

        mycell = SpinyStellate(proto, sim.model.path + "/SpinyStellate")
        print 'Cell created'
        for handler in config.LOGGER.handlers:
            handler.flush()


        mycell.soma.x0 = 0.0
        mycell.soma.y0 = 0.0
        mycell.soma.z0 = 0.0
        mycell.soma.x = 0.0
        mycell.soma.y = 0.0
        mycell.soma.z = mycell.soma.length
        # mycellview = MyCellView(mycell)
        config.LOGGER.debug('Created cell: %s' % (mycell.path))
        # for neighbour in mycell.soma.neighbours('raxial'):
        #     print 'RAXIAL', neighbours.path()
        # for neighbour in mycell.soma.neighbours('axial'):
        #     print 'AXIAL', neighbour.path()
        vm_table = mycell.comp[mycell.presyn].insertRecorder('Vm_spinstell', 'Vm', sim.data)
        pulsegen = mycell.soma.insertPulseGen('pulsegen', sim.model, firstLevel=3e-10, firstDelay=50e-3, firstWidth=50e-3)
#         pulsegen1 = mycell.soma.insertPulseGen('pulsegen1', sim.model, firstLevel=3e-7, firstDelay=150e-3, firstWidth=10e-3)

        sim.schedule()
        if mycell.has_cycle():
            print "WARNING!! CYCLE PRESENT IN CICRUIT."
        t1 = datetime.now()
        sim.run(200e-3)
        t2 = datetime.now()
        delta = t2 - t1
        print 'simulation time: ', delta.seconds + 1e-6 * delta.microseconds
        sim.dump_data('data')
        if config.has_pylab:
            mus_vm = config.pylab.array(vm_table) * 1e3
            mus_t = linspace(0, sim.simtime * 1e3, len(mus_vm))
            try:
                nrn_vm = config.pylab.loadtxt('../nrn/mydata/Vm_spinstell.plot')
                nrn_t = nrn_vm[:, 0]
                nrn_vm = nrn_vm[:, 1]
                config.pylab.plot(nrn_t, nrn_vm, 'y-', label='nrn vm')
            except IOError:
                print 'NEURON Data not available.'
            config.pylab.plot(mus_t, mus_vm, 'g-.', label='mus vm')
            config.pylab.legend()
            config.pylab.show()

# 需要导入模块: from simulation import Simulation [as 别名]
# 或者: from simulation.Simulation import dump_data [as 别名]
    def test_single_cell(cls):
        """Simulates a single spiny stellate cell and plots the Vm and
        [Ca2+]"""

        config.LOGGER.info("/**************************************************************************")
        config.LOGGER.info(" *")
        config.LOGGER.info(" * Simulating a single cell: %s" % (cls.__name__))
        config.LOGGER.info(" *")
        config.LOGGER.info(" **************************************************************************/")
        sim = Simulation(cls.__name__)
        proto = TraubCell.read_proto("SpinyStellate.p", "SpinyStellate_1", SpinyStellate.chan_params)
        print 'Model path', sim.model.path , 'proto', proto

        mycell = SpinyStellate(proto, sim.model.path + "/SpinyStellate")
        print 'Cell created'
        for handler in config.LOGGER.handlers:
            handler.flush()


        config.LOGGER.debug('Created cell: %s' % (mycell.path))
        # for neighbour in mycell.soma.neighbours('raxial'):
        #     print 'RAXIAL', neighbours.path()
        # for neighbour in mycell.soma.neighbours('axial'):
        #     print 'AXIAL', neighbour.path()
        vm_table = mycell.comp[mycell.presyn].insertRecorder('Vm_spinstell', 'Vm', sim.data)
        pulsegen = mycell.soma.insertPulseGen('pulsegen', sim.model, firstLevel=3e-10, firstDelay=100e-3, firstWidth=200e-3)
#         pulsegen1 = mycell.soma.insertPulseGen('pulsegen1', sim.model, firstLevel=3e-7, firstDelay=150e-3, firstWidth=10e-3)

        sim.schedule()
        if mycell.has_cycle():
            config.LOGGER.warning("WARNING!! CYCLE PRESENT IN CICRUIT.")
        t1 = datetime.now()
        sim.run(0.5)
        t2 = datetime.now()
        delta = t2 - t1
        config.BENCHMARK_LOGGER.info('simulation time: %g' % (delta.seconds + 1e-6 * delta.microseconds))
        for msg in moose.Neutral('/model/SpinyStellate/solve').inMessages():
            print msg
        for msg in moose.Neutral('/model/SpinyStellate/solve').outMessages():
            print msg
        sim.dump_data('data')
        # mycell.dump_cell('spinstell.txt')
        if config.has_pylab:
            mus_vm = config.pylab.array(vm_table) * 1e3
            mus_t = linspace(0, sim.simtime*1e3, len(mus_vm))
            config.pylab.plot(mus_t, mus_vm, 'g-.', label='mus vm')
            try:
                nrn_vm = config.pylab.loadtxt('../nrn/mydata/Vm_spinstell.plot')
                nrn_t = nrn_vm[:, 0]
                nrn_vm = nrn_vm[:, 1]
                nrn_ca = config.pylab.loadtxt('../nrn/mydata/Ca_spinstell.plot')
                config.pylab.plot(nrn_t, nrn_vm, 'y-', label='nrn vm')
            except IOError:
                pass
            config.pylab.legend(loc=0)
            config.pylab.title('spinystellate')
            config.pylab.show()

# 需要导入模块: from simulation import Simulation [as 别名]
# 或者: from simulation.Simulation import dump_data [as 别名]
    def test_single_cell(cls):
        """Simulates a single tufted intrinsically bursting cell and
        plots the Vm and [Ca2+]"""

        config.LOGGER.info("/**************************************************************************")
        config.LOGGER.info(" *")
        config.LOGGER.info(" * Simulating a single cell: %s" % (cls.__name__))
        config.LOGGER.info(" *")
        config.LOGGER.info(" **************************************************************************/")
        sim = Simulation(cls.__name__)
        mycell = TuftedIB(TuftedIB.prototype, sim.model.path + "/TuftedIB")
        print 'Created cell:', mycell.path
        vm_table = mycell.comp[mycell.presyn].insertRecorder('Vm_tuftIB', 'Vm', sim.data)
        ca_conc_path = mycell.soma.path + '/CaPool'
        ca_table = None
        if config.context.exists(ca_conc_path):
            ca_conc = moose.CaConc(ca_conc_path)
            ca_table = moose.Table('Ca_tuftIB', sim.data)
            ca_table.stepMode = 3
            ca_conc.connect('Ca', ca_table, 'inputRequest')
        kc_path = mycell.soma.path + '/KC'
        gk_table = None
        if config.context.exists(kc_path):
            gk_table = moose.Table('gkc', sim.data)
            gk_table.stepMode = 3
            kc = moose.HHChannel(kc_path)
            kc.connect('Gk', gk_table, 'inputRequest')
            pymoose.showmsg(ca_conc)
        pulsegen = mycell.soma.insertPulseGen('pulsegen', sim.model, firstLevel=0.3e-9, firstDelay=0.0, firstWidth=50e-3)
#         pulsegen1 = mycell.soma.insertPulseGen('pulsegen1', sim.model, firstLevel=3e-7, firstDelay=150e-3, firstWidth=10e-3)

        sim.schedule()
        if mycell.has_cycle():
            print "WARNING!! CYCLE PRESENT IN CICRUIT."
        t1 = datetime.now()
        sim.run(200e-3)
        t2 = datetime.now()
        delta = t2 - t1
        print 'simulation time: ', delta.seconds + 1e-6 * delta.microseconds
        sim.dump_data('data')
        if config.has_pylab:
            mus_vm = config.pylab.array(vm_table) * 1e3
            mus_t = linspace(0, sim.simtime * 1e3, len(mus_vm))
            try:
                nrn_vm = config.pylab.loadtxt('../nrn/mydata/Vm_deepLTS.plot')
                nrn_t = nrn_vm[:, 0]
                nrn_vm = nrn_vm[:, 1]
                config.pylab.plot(nrn_t, nrn_vm, 'y-', label='nrn vm')
            except IOError:
                print 'NEURON Data not available.'
            config.pylab.plot(mus_t, mus_vm, 'g-.', label='mus vm')
            config.pylab.legend()
            config.pylab.show()

# 需要导入模块: from simulation import Simulation [as 别名]
# 或者: from simulation.Simulation import dump_data [as 别名]
def test_full_model(simtime, simdt=1e-4, plotdt=1e-3, cell_count=None):
    """Setup and run the full Traub model"""
    sim = Simulation('traub')
    net = []
    scale = 10
    if cell_count is None:
        cell_count = CELL_COUNT
    network = Network(sim, cell_count)
    network.setup_random_recording(0.05) # record from 5% of cells
    sim.schedule(simdt=simdt, plotdt=plotdt, gldt=1e10)
    sim.run(time=simtime)
    sim.dump_data(config.data_dir, True)

# 需要导入模块: from simulation import Simulation [as 别名]
# 或者: from simulation.Simulation import dump_data [as 别名]
def inject_test(celltype, current_list, simtime=2.0):
    test_data = {}
    sim = Simulation(celltype)
    for ii, current in enumerate(current_list):
        test_data[ii] = setup_model(ii, celltype, current, sim)
    sim.schedule()
    sim.run(simtime)
    sim.dump_data('data')
    timeseries = np.linspace(0, simtime, len(test_data[0]['Vm']))
    for ii, current in enumerate(current_list):
        color = cmap(ii*1.0/len(current_list), len(current_list))
        plt.plot(timeseries * 1e3, np.array(test_data[ii]['Vm']) * 1e3, color=color, label='%g nA' % (current * 1e9))
    plt.legend()
    plt.show()

# 需要导入模块: from simulation import Simulation [as 别名]
# 或者: from simulation.Simulation import dump_data [as 别名]
    def test_single_cell(cls):
        """Simulates a single superficial pyramidal regular spiking
        cell and plots the Vm and [Ca2+]"""

        config.LOGGER.info("/**************************************************************************")
        config.LOGGER.info(" *")
        config.LOGGER.info(" * Simulating a single cell: %s" % (cls.__name__))
        config.LOGGER.info(" *")
        config.LOGGER.info(" **************************************************************************/")
        sim = Simulation(cls.__name__)
        sim.simdt = 5e-6
        sim.plotdt = 1e-4
        mycell = SupPyrRS(SupPyrRS.prototype, sim.model.path + "/SupPyrRS")
        config.LOGGER.info('Created cell: %s' % (mycell.path))
        vm_table = mycell.comp[mycell.presyn].insertRecorder('Vm_suppyrRS', 'Vm', sim.data)
        pulsegen = mycell.soma.insertPulseGen('pulsegen', sim.model, firstLevel=0.3e-9, firstDelay=100e-3, firstWidth=200e-3)
        sim.schedule()
        if mycell.has_cycle():
            config.LOGGER.warning("WARNING!! CYCLE PRESENT IN CICRUIT.")
        t1 = datetime.now()
        sim.run(500e-3)
        t2 = datetime.now()
        sim.dump_data('data')
        delta = t2 - t1
        config.BENCHMARK_LOGGER.info('simulation time: %g' % (delta.seconds + 1e-6 * delta.microseconds))
        if config.has_pylab:
            mus_vm = config.pylab.array(vm_table) * 1e3
            mus_t = linspace(0, sim.simtime*1e3, len(mus_vm))
            try:
                nrn_vm = config.pylab.loadtxt('../nrn/mydata/Vm_suppyrrs.plot')
                nrn_t = nrn_vm[:, 0]
                nrn_vm = nrn_vm[:, 1]
                # nrn_ca = config.pylab.loadtxt('../nrn/mydata/Ca_suppyrrs.plot')
                # nrn_ca = nrn_ca[:,1]
                config.pylab.plot(nrn_t, nrn_vm, 'y-', label='nrn vm')
            except IOError:
                pass
            data = config.pylab.zeros((len(mus_vm), 2))
            data[:, 0] = mus_t[:]
            data[:, 1] = mus_vm[:]
            
            config.pylab.plot(mus_t, mus_vm, 'g-.', label='mus vm')
            # if ca_table:
            #     ca_array = config.pylab.array(ca_table)
            #     config.pylab.plot(nrn_t, -nrn_ca, 'r-', label='nrn (-)ca')
            #     config.pylab.plot(mus_t, -ca_array, 'b-.', label='mus (-)ca')
            #     print config.pylab.amax(ca_table)
            config.pylab.legend()
            config.pylab.title('suppyrRS')
            config.pylab.show()

# 需要导入模块: from simulation import Simulation [as 别名]
# 或者: from simulation.Simulation import dump_data [as 别名]
    def test_single_cell(cls):
        """Simulates a single nRT cell and plots the Vm and [Ca2+]"""

        config.LOGGER.info("/**************************************************************************")
        config.LOGGER.info(" *")
        config.LOGGER.info(" * Simulating a single cell: %s" % (cls.__name__))
        config.LOGGER.info(" *")
        config.LOGGER.info(" **************************************************************************/")
        sim = Simulation(cls.__name__)
        mycell = SupBasket(SupBasket.prototype, sim.model.path + "/SupBasket")
        print "Created cell:", mycell.path
        vm_table = mycell.comp[mycell.presyn].insertRecorder("Vm_supbask", "Vm", sim.data)
        pulsegen = mycell.soma.insertPulseGen(
            "pulsegen", sim.model, firstLevel=3e-10, firstDelay=100e-3, firstWidth=200e-3
        )
        #         pulsegen1 = mycell.soma.insertPulseGen('pulsegen1', sim.model, firstLevel=3e-7, firstDelay=150e-3, firstWidth=10e-3)

        sim.schedule()
        if mycell.has_cycle():
            print "WARNING!! CYCLE PRESENT IN CICRUIT."
        t1 = datetime.now()
        sim.run(500e-3)
        t2 = datetime.now()
        delta = t2 - t1
        print "simulation time: ", delta.seconds + 1e-6 * delta.microseconds
        sim.dump_data("data")
        mycell.dump_cell("supbask.txt")
        if config.has_pylab:
            mus_vm = config.pylab.array(vm_table) * 1e3
            nrn_vm = config.pylab.loadtxt("../nrn/mydata/Vm_supbask.plot")
            nrn_t = nrn_vm[:, 0]
            mus_t = linspace(0, nrn_t[-1], len(mus_vm))
            nrn_vm = nrn_vm[:, 1]
            nrn_ca = config.pylab.loadtxt("../nrn/mydata/Ca_supbask.plot")
            nrn_ca = nrn_ca[:, 1]
            config.pylab.plot(nrn_t, nrn_vm, "y-", label="nrn vm")
            config.pylab.plot(mus_t, mus_vm, "g-.", label="mus vm")
            #         if ca_table:
            #             ca_array = config.pylab.array(ca_table)
            #             config.pylab.plot(nrn_t, -nrn_ca, 'r-', label='nrn (-)ca')
            #             config.pylab.plot(mus_t, -ca_array, 'b-.', label='mus (-)ca')
            #             print config.pylab.amax(ca_table)
            config.pylab.legend()
            config.pylab.title("supbasket")
            config.pylab.show()

# 需要导入模块: from simulation import Simulation [as 别名]
# 或者: from simulation.Simulation import dump_data [as 别名]
    def test_single_cell(cls):
        """Simulates a single superficial LTS cell and plots the Vm and [Ca2+]"""

        config.LOGGER.info("/**************************************************************************")
        config.LOGGER.info(" *")
        config.LOGGER.info(" * Simulating a single cell: %s" % (cls.__name__))
        config.LOGGER.info(" *")
        config.LOGGER.info(" **************************************************************************/")
        sim = Simulation(cls.__name__)
        mycell = SupLTS(SupLTS.prototype, sim.model.path + "/SupLTS")
        print 'Created cell:', mycell.path
        vm_table = mycell.comp[mycell.presyn].insertRecorder('Vm_supLTS', 'Vm', sim.data)
        ca_conc_path = mycell.soma.path + '/CaPool'
        ca_table = None
        if config.context.exists(ca_conc_path):
            ca_conc = moose.CaConc(ca_conc_path)
            ca_table = moose.Table('Ca_supLTS', sim.data)
            ca_table.stepMode = 3
            ca_conc.connect('Ca', ca_table, 'inputRequest')
        pulsegen = mycell.soma.insertPulseGen('pulsegen', sim.model, firstLevel=3e-10, firstDelay=100e-3, firstWidth=200e-3)
        sim.schedule()
        if mycell.has_cycle():
            print "WARNING!! CYCLE PRESENT IN CICRUIT."
        t1 = datetime.now()
        sim.run(500e-3)
        t2 = datetime.now()
        delta = t2 - t1
        print 'simulation time: ', delta.seconds + 1e-6 * delta.microseconds
        sim.dump_data('data')
        mycell.dump_cell('supLTS.txt')
        if config.has_pylab:
            mus_vm = config.pylab.array(vm_table) * 1e3
            nrn_vm = config.pylab.loadtxt('../nrn/mydata/Vm_supLTS.plot')
            nrn_t = nrn_vm[:, 0]
            mus_t = linspace(0, sim.simtime*1e3, len(mus_vm))
            nrn_vm = nrn_vm[:, 1]
            nrn_ca = config.pylab.loadtxt('../nrn/mydata/Ca_supLTS.plot')
            nrn_ca = nrn_ca[:,1]
            title = 'SupLTS:'
            config.pylab.title(title)
            config.pylab.plot(nrn_t, nrn_vm, 'y-', label='nrn vm')
            config.pylab.plot(mus_t, mus_vm, 'g-.', label='mus vm')
            config.pylab.legend()
            config.pylab.title('supLTS')
            config.pylab.show()

# 需要导入模块: from simulation import Simulation [as 别名]
# 或者: from simulation.Simulation import dump_data [as 别名]
    def test_single_cell(cls):
        """Simulates a single thalamocortical relay cell
        and plots the Vm and [Ca2+]"""

        config.LOGGER.info("/**************************************************************************")
        config.LOGGER.info(" *")
        config.LOGGER.info(" * Simulating a single cell: %s" % (cls.__name__))
        config.LOGGER.info(" *")
        config.LOGGER.info(" **************************************************************************/")
        sim = Simulation(cls.__name__)
        sim.simdt = 5e-6
        sim.plotdt = 0.5e-4
        mycell = TCR(TCR.prototype, sim.model.path + "/TCR")
        # for ii in range(1, mycell.num_comp):
        #     mycell.comp[ii].Em = -57e-3
        print 'Created cell:', mycell.path
        vm_table_presyn = mycell.comp[mycell.presyn].insertRecorder('Vm_TCR', 'Vm', sim.data)
        vm_table_soma = mycell.soma.insertRecorder('TCR_soma_Vm', 'Vm', sim.data)
        print 'Tables created:', vm_table_soma.path, vm_table_presyn.path
        stim_table = moose.Table('%s/stimulus' % (sim.data.path))
        stim_table.stepMode = 3
        pulsegen = mycell.soma.insertPulseGen('pulsegen', sim.model, firstLevel=-1e-9, firstDelay=100e-3, firstWidth=100e-3)
        pulsegen.secondDelay = 200e-3
        pulsegen.secondWidth = 100e-3
        pulsegen.secondLevel = 0.3e-9
        pulsegen.count = 3
        pulsegen.delay[2] = 1e9
        # pulsegen.count = 4
        # for ii in range(pulsegen.count):
        #     pulsegen.delay[ii] = 0.025
        #     pulsegen.level[ii] = 1e-9
        #     pulsegen.width[ii] = 100e-6
        # pulsegen.delay[0]= 3.0
        stim_table.connect('inputRequest', pulsegen, 'output')
    
        sim.schedule()
        if mycell.has_cycle():
            print "WARNING!! CYCLE PRESENT IN CICRUIT."
        t1 = datetime.now()
        sim.run(0.5)
        t2 = datetime.now()
        delta = t2 - t1
        print 'simulation time: ', delta.seconds + 1e-6 * delta.microseconds
        sim.dump_data('data')

# 需要导入模块: from simulation import Simulation [as 别名]
# 或者: from simulation.Simulation import dump_data [as 别名]
    def test_single_cell(cls):
        """Simulates a single superficial axo-axonic cell and plots
        the Vm and [Ca2+]"""

        config.LOGGER.info("/**************************************************************************")
        config.LOGGER.info(" *")
        config.LOGGER.info(" * Simulating a single cell: %s" % (cls.__name__))
        config.LOGGER.info(" *")
        config.LOGGER.info(" **************************************************************************/")
        sim = Simulation(cls.__name__)
        mycell = SupAxoaxonic(SupAxoaxonic.prototype, sim.model.path + "/SupAxoaxonic")
        print 'Created cell:', mycell.path
        vm_table = mycell.comp[mycell.presyn].insertRecorder('Vm_supaxax', 'Vm', sim.data)
        pulsegen = mycell.soma.insertPulseGen('pulsegen', sim.model, firstLevel=3e-10, firstDelay=100e-3, firstWidth=200e-3)
#         pulsegen1 = mycell.soma.insertPulseGen('pulsegen1', sim.model, firstLevel=3e-7, firstDelay=150e-3, firstWidth=10e-3)

        sim.schedule()
        if mycell.has_cycle():
            print "WARNING!! CYCLE PRESENT IN CICRUIT."
        t1 = datetime.now()
        sim.run(500e-3)
        t2 = datetime.now()
        delta = t2 - t1
        print 'simulation time: ', delta.seconds + 1e-6 * delta.microseconds
        sim.dump_data('data')
        mycell.dump_cell('supaxax.txt')
        if config.has_pylab:
            mus_vm = config.pylab.array(vm_table) * 1e3
            nrn_vm = config.pylab.loadtxt('../nrn/mydata/Vm_supaxax.plot')
            nrn_t = nrn_vm[:, 0]
            mus_t = linspace(0, nrn_t[-1], len(mus_vm))
            nrn_vm = nrn_vm[:, 1]
            nrn_ca = config.pylab.loadtxt('../nrn/mydata/Ca_supaxax.plot')
            nrn_ca = nrn_ca[:,1]
            config.pylab.plot(nrn_t, nrn_vm, 'y-', label='nrn vm')
            config.pylab.plot(mus_t, mus_vm, 'g-.', label='mus vm')
    #         if ca_table:
    #             ca_array = config.pylab.array(ca_table)
    #             config.pylab.plot(nrn_t, -nrn_ca, 'r-', label='nrn (-)ca')
    #             config.pylab.plot(mus_t, -ca_array, 'b-.', label='mus (-)ca')
    #             print config.pylab.amax(ca_table)
            config.pylab.legend()
            config.pylab.title('supaxoaxonic')
            config.pylab.show()

# 需要导入模块: from simulation import Simulation [as 别名]
# 或者: from simulation.Simulation import dump_data [as 别名]
    def test_single_cell(cls):
        """Simulates a single nRT cell and plots the Vm and [Ca2+]"""

        config.LOGGER.info("/**************************************************************************")
        config.LOGGER.info(" *")
        config.LOGGER.info(" * Simulating a single cell: %s" % (cls.__name__))
        config.LOGGER.info(" *")
        config.LOGGER.info(" **************************************************************************/")
        sim = Simulation(cls.__name__)
        mycell = nRT(nRT.prototype, sim.model.path + "/nRT")
        config.LOGGER.info('Created cell: %s' % (mycell.path))
        vm_table = mycell.comp[mycell.presyn].insertRecorder('Vm_nRT', 'Vm', sim.data)
        pulsegen = mycell.soma.insertPulseGen('pulsegen', sim.model, firstLevel=3e-10, firstDelay=100.0e-3, firstWidth=200e-3)
#         pulsegen1 = mycell.soma.insertPulseGen('pulsegen1', sim.model, firstLevel=3e-7, firstDelay=150e-3, firstWidth=10e-3)

        sim.schedule()
        if mycell.has_cycle():
            config.LOGGING.warning("WARNING!! CYCLE PRESENT IN CICRUIT.")
        t1 = datetime.now()
        sim.run(500e-3)
        t2 = datetime.now()
        delta = t2 - t1
        config.LOGGER.info('simulation time: %g'  % (delta.seconds + 1e-6 * delta.microseconds))
        sim.dump_data('data')
        mycell.dump_cell('nRT.txt')        
        if config.has_pylab:
            mus_vm = config.pylab.array(vm_table) * 1e3
            mus_t = linspace(0, sim.simtime*1e3, len(mus_vm))
            try:
                nrn_vm = config.pylab.loadtxt('../nrn/mydata/Vm_nRT.plot')
                print 'Here', nrn_vm.shape
                nrn_t = nrn_vm[:, 0]
                nrn_vm = nrn_vm[:, 1]
                config.pylab.plot(nrn_t, nrn_vm, 'y-', label='nrn vm')
            except IOError:
                pass
            print mus_vm.shape, mus_t.shape
            config.pylab.plot(mus_t, mus_vm, 'g-.', label='mus vm')
            config.pylab.legend()
            config.pylab.title('nRT')
            config.pylab.show()

# 需要导入模块: from simulation import Simulation [as 别名]
# 或者: from simulation.Simulation import dump_data [as 别名]
    def test_single_cell(cls):
        """Simulates a single nontufted regular spiking cell and plots
        the Vm and [Ca2+]"""

        config.LOGGER.info("/**************************************************************************")
        config.LOGGER.info(" *")
        config.LOGGER.info(" * Simulating a single cell: %s" % (cls.__name__))
        config.LOGGER.info(" *")
        config.LOGGER.info(" **************************************************************************/")

        sim = Simulation(cls.__name__)
        mycell = NontuftedRS(NontuftedRS.prototype, sim.model.path + "/NontuftedRS")
        print 'Created cell:', mycell.path
        vm_table = mycell.comp[NontuftedRS.presyn].insertRecorder('Vm_nontuftRS', 'Vm', sim.data)
        pulsegen = mycell.soma.insertPulseGen('pulsegen', sim.model, firstLevel=1e-9, firstDelay=100e-3, firstWidth=200e-3)
        sim.schedule()
        if mycell.has_cycle():
            print "WARNING!! CYCLE PRESENT IN CICRUIT."
        t1 = datetime.now()
        sim.run(0.5)
        t2 = datetime.now()
        delta = t2 - t1
        print 'simulation time: ', delta.seconds + 1e-6 * delta.microseconds
        sim.dump_data('data')
        if config.has_pylab:
            mus_vm = config.pylab.array(vm_table) * 1e3
            mus_t = linspace(0, sim.simtime*1e3, len(mus_vm))
            config.pylab.plot(mus_t, mus_vm, 'g-.', label='mus vm')
            try:
                nrn_vm = config.pylab.loadtxt('../nrn/mydata/Vm_nontuftRS.plot')
                nrn_t = nrn_vm[:, 0]
                nrn_vm = nrn_vm[:, 1]
                config.pylab.plot(nrn_t, nrn_vm, 'y-', label='nrn vm')
            except IOError:
                pass
            config.pylab.legend()
            config.pylab.title('nontuftedRS')
            config.pylab.show()