In [1]:
from mpl_toolkits.mplot3d import Axes3D
%pylab nbagg
from tvb.simulator.lab import *
Populating the interactive namespace from numpy and matplotlib
INFO NumExpr defaulting to 3 threads.
WARNING Field seems mutable and has a default value. Consider using a lambda as a value factory
attribute tvb.simulator.models.epileptor.Epileptor.state_variable_range = Final(field_type=<class 'dict'>, default={'x1': array([-2., 1.]), 'y1': array([-20., 2.]), 'z': array([2., 5.]), 'x2': array([-2., 0.]), 'y2': array([0., 2.]), 'g': array([-1., 1.])}, required=True)
WARNING default contains values out of the declared domain. Ex 1.0
attribute tvb.simulator.models.epileptor.Epileptor2D.tt = NArray(label='tt', dtype=float64, default=array([1.]), dim_names=(), ndim=None, required=True)
WARNING Field seems mutable and has a default value. Consider using a lambda as a value factory
attribute tvb.simulator.models.epileptor.Epileptor2D.state_variable_range = Final(field_type=<class 'dict'>, default={'x1': array([-2., 1.]), 'z': array([2., 5.])}, required=True)
WARNING default contains values out of the declared domain. Ex 1.0
attribute tvb.simulator.models.epileptor_rs.EpileptorRestingState.gamma_rs = NArray(label=":math:'\\gamma_rs'", dtype=float64, default=array([1.]), dim_names=(), ndim=None, required=True)
WARNING Field seems mutable and has a default value. Consider using a lambda as a value factory
attribute tvb.simulator.models.epileptor_rs.EpileptorRestingState.state_variable_range = Final(field_type=<class 'dict'>, default={'x1': array([-1.8, -1.4]), 'y1': array([-15, -10]), 'z': array([3.6, 4. ]), 'x2': array([-1.1, -0.9]), 'y2': array([0.001, 0.01 ]), 'g': array([-1., 1.]), 'x_rs': array([-2., 4.]), 'y_rs': array([-6., 6.])}, required=True)
WARNING Field seems mutable and has a default value. Consider using a lambda as a value factory
attribute tvb.simulator.models.epileptorcodim3.EpileptorCodim3.state_variable_range = Final(field_type=<class 'dict'>, default={'x': array([0.4, 0.6]), 'y': array([-0.1, 0.1]), 'z': array([0. , 0.15])}, required=True)
WARNING Field seems mutable and has a default value. Consider using a lambda as a value factory
attribute tvb.simulator.models.epileptorcodim3.EpileptorCodim3SlowMod.state_variable_range = Final(field_type=<class 'dict'>, default={'x': array([0.4, 0.6]), 'y': array([-0.1, 0.1]), 'z': array([0. , 0.1]), 'uA': array([0., 0.]), 'uB': array([0., 0.])}, required=True)
WARNING Field seems mutable and has a default value. Consider using a lambda as a value factory
attribute tvb.simulator.models.hopfield.Hopfield.state_variable_range = Final(field_type=<class 'dict'>, default={'x': array([-1., 2.]), 'theta': array([0., 1.])}, required=True)
WARNING default contains values out of the declared domain. Ex 0.12
attribute tvb.simulator.models.jansen_rit.JansenRit.p_min = NArray(label=':math:`p_{min}`', dtype=float64, default=array([0.12]), dim_names=(), ndim=None, required=True)
WARNING default contains values out of the declared domain. Ex 0.32
attribute tvb.simulator.models.jansen_rit.JansenRit.p_max = NArray(label=':math:`p_{max}`', dtype=float64, default=array([0.32]), dim_names=(), ndim=None, required=True)
WARNING default contains values out of the declared domain. Ex 0.22
attribute tvb.simulator.models.jansen_rit.JansenRit.mu = NArray(label=':math:`\\mu_{max}`', dtype=float64, default=array([0.22]), dim_names=(), ndim=None, required=True)
WARNING Field seems mutable and has a default value. Consider using a lambda as a value factory
attribute tvb.simulator.models.jansen_rit.JansenRit.state_variable_range = Final(field_type=<class 'dict'>, default={'y0': array([-1., 1.]), 'y1': array([-500., 500.]), 'y2': array([-50., 50.]), 'y3': array([-6., 6.]), 'y4': array([-20., 20.]), 'y5': array([-500., 500.])}, required=True)
WARNING Field seems mutable and has a default value. Consider using a lambda as a value factory
attribute tvb.simulator.models.jansen_rit.ZetterbergJansen.state_variable_range = Final(field_type=<class 'dict'>, default={'v1': array([-100., 100.]), 'y1': array([-500., 500.]), 'v2': array([-100., 50.]), 'y2': array([-100., 6.]), 'v3': array([-100., 6.]), 'y3': array([-100., 6.]), 'v4': array([-100., 20.]), 'y4': array([-100., 20.]), 'v5': array([-100., 20.]), 'y5': array([-500., 500.]), 'v6': array([-100., 20.]), 'v7': array([-100., 20.])}, required=True)
WARNING default contains values out of the declared domain. Ex -0.01
attribute tvb.simulator.models.larter_breakspear.LarterBreakspear.TCa = NArray(label=':math:`T_{Ca}`', dtype=float64, default=array([-0.01]), dim_names=(), ndim=None, required=True)
WARNING default contains values out of the declared domain. Ex 0.3
attribute tvb.simulator.models.larter_breakspear.LarterBreakspear.TNa = NArray(label=':math:`T_{Na}`', dtype=float64, default=array([0.3]), dim_names=(), ndim=None, required=True)
WARNING default contains values out of the declared domain. Ex 2.0
attribute tvb.simulator.models.larter_breakspear.LarterBreakspear.aei = NArray(label=':math:`a_{ei}`', dtype=float64, default=array([2.]), dim_names=(), ndim=None, required=True)
WARNING default contains values out of the declared domain. Ex 2.0
attribute tvb.simulator.models.larter_breakspear.LarterBreakspear.aie = NArray(label=':math:`a_{ie}`', dtype=float64, default=array([2.]), dim_names=(), ndim=None, required=True)
WARNING default contains values out of the declared domain. Ex 1.0
attribute tvb.simulator.models.larter_breakspear.LarterBreakspear.ane = NArray(label=':math:`a_{ne}`', dtype=float64, default=array([1.]), dim_names=(), ndim=None, required=True)
WARNING default contains values out of the declared domain. Ex 0.3
attribute tvb.simulator.models.larter_breakspear.LarterBreakspear.Iext = NArray(label=':math:`I_{ext}`', dtype=float64, default=array([0.3]), dim_names=(), ndim=None, required=True)
WARNING default contains values out of the declared domain. Ex 1.0
attribute tvb.simulator.models.larter_breakspear.LarterBreakspear.QV_max = NArray(label=':math:`Q_{max}`', dtype=float64, default=array([1.]), dim_names=(), ndim=None, required=True)
WARNING default contains values out of the declared domain. Ex 1.0
attribute tvb.simulator.models.larter_breakspear.LarterBreakspear.QZ_max = NArray(label=':math:`Q_{max}`', dtype=float64, default=array([1.]), dim_names=(), ndim=None, required=True)
WARNING default contains values out of the declared domain. Ex 1.0
attribute tvb.simulator.models.larter_breakspear.LarterBreakspear.t_scale = NArray(label=':math:`t_{scale}`', dtype=float64, default=array([1.]), dim_names=(), ndim=None, required=True)
WARNING Field seems mutable and has a default value. Consider using a lambda as a value factory
attribute tvb.simulator.models.larter_breakspear.LarterBreakspear.state_variable_range = Final(field_type=<class 'dict'>, default={'V': array([-1.5, 1.5]), 'W': array([-1.5, 1.5]), 'Z': array([-1.5, 1.5])}, required=True)
WARNING Field seems mutable and has a default value. Consider using a lambda as a value factory
attribute tvb.simulator.models.linear.Linear.state_variable_range = Final(field_type=<class 'dict'>, default={'x': array([-1, 1])}, required=True)
WARNING default contains values out of the declared domain. Ex 1.0
attribute tvb.simulator.models.oscillator.Generic2dOscillator.gamma = NArray(label=':math:`\\gamma`', dtype=float64, default=array([1.]), dim_names=(), ndim=None, required=True)
WARNING Field seems mutable and has a default value. Consider using a lambda as a value factory
attribute tvb.simulator.models.oscillator.Generic2dOscillator.state_variable_range = Final(field_type=<class 'dict'>, default={'V': array([-2., 4.]), 'W': array([-6., 6.])}, required=True)
WARNING Field seems mutable and has a default value. Consider using a lambda as a value factory
attribute tvb.simulator.models.oscillator.Kuramoto.state_variable_range = Final(field_type=<class 'dict'>, default={'theta': array([0. , 6.28318531])}, required=True)
WARNING Field seems mutable and has a default value. Consider using a lambda as a value factory
attribute tvb.simulator.models.oscillator.SupHopf.state_variable_range = Final(field_type=<class 'dict'>, default={'x': array([-5., 5.]), 'y': array([-5., 5.])}, required=True)
WARNING Field seems mutable and has a default value. Consider using a lambda as a value factory
attribute tvb.simulator.models.stefanescu_jirsa.ReducedSetFitzHughNagumo.state_variable_range = Final(field_type=<class 'dict'>, default={'xi': array([-4., 4.]), 'eta': array([-3., 3.]), 'alpha': array([-4., 4.]), 'beta': array([-3., 3.])}, required=True)
WARNING default contains values out of the declared domain. Ex 1.0
attribute tvb.simulator.models.stefanescu_jirsa.ReducedSetHindmarshRose.a = NArray(label=':math:`a`', dtype=float64, default=array([1.]), dim_names=(), ndim=None, required=True)
WARNING default contains values out of the declared domain. Ex 3.0
attribute tvb.simulator.models.stefanescu_jirsa.ReducedSetHindmarshRose.b = NArray(label=':math:`b`', dtype=float64, default=array([3.]), dim_names=(), ndim=None, required=True)
WARNING default contains values out of the declared domain. Ex 1.0
attribute tvb.simulator.models.stefanescu_jirsa.ReducedSetHindmarshRose.c = NArray(label=':math:`c`', dtype=float64, default=array([1.]), dim_names=(), ndim=None, required=True)
WARNING default contains values out of the declared domain. Ex 3.3
attribute tvb.simulator.models.stefanescu_jirsa.ReducedSetHindmarshRose.mu = NArray(label=':math:`\\mu`', dtype=float64, default=array([3.3]), dim_names=(), ndim=None, required=True)
WARNING Field seems mutable and has a default value. Consider using a lambda as a value factory
attribute tvb.simulator.models.stefanescu_jirsa.ReducedSetHindmarshRose.state_variable_range = Final(field_type=<class 'dict'>, default={'xi': array([-4., 4.]), 'eta': array([-25., 20.]), 'tau': array([ 2., 10.]), 'alpha': array([-4., 4.]), 'beta': array([-20., 20.]), 'gamma': array([ 2., 10.])}, required=True)
WARNING Field seems mutable and has a default value. Consider using a lambda as a value factory
attribute tvb.simulator.models.wilson_cowan.WilsonCowan.state_variable_range = Final(field_type=<class 'dict'>, default={'E': array([0., 1.]), 'I': array([0., 1.])}, required=True)
WARNING default contains values out of the declared domain. Ex 0.27
attribute tvb.simulator.models.wong_wang.ReducedWongWang.a = NArray(label=':math:`a`', dtype=float64, default=array([0.27]), dim_names=(), ndim=None, required=True)
WARNING Field seems mutable and has a default value. Consider using a lambda as a value factory
attribute tvb.simulator.models.wong_wang.ReducedWongWang.state_variable_range = Final(field_type=<class 'dict'>, default={'S': array([0., 1.])}, required=True)
WARNING Field seems mutable and has a default value. Consider using a lambda as a value factory
attribute tvb.simulator.models.wong_wang.ReducedWongWang.state_variable_boundaries = Final(field_type=<class 'dict'>, default={'S': array([0., 1.])}, required=True)
WARNING default contains values out of the declared domain. Ex 10.0
attribute tvb.simulator.models.wong_wang_exc_inh.ReducedWongWangExcInh.tau_i = NArray(label=':math:`\\tau_i`', dtype=float64, default=array([10.]), dim_names=(), ndim=None, required=True)
WARNING Field seems mutable and has a default value. Consider using a lambda as a value factory
attribute tvb.simulator.models.wong_wang_exc_inh.ReducedWongWangExcInh.state_variable_range = Final(field_type=<class 'dict'>, default={'S_e': array([0., 1.]), 'S_i': array([0., 1.])}, required=True)
WARNING Field seems mutable and has a default value. Consider using a lambda as a value factory
attribute tvb.simulator.models.wong_wang_exc_inh.ReducedWongWangExcInh.state_variable_boundaries = Final(field_type=<class 'dict'>, default={'S_e': array([0., 1.]), 'S_i': array([0., 1.])}, required=True)
WARNING Field seems mutable and has a default value. Consider using a lambda as a value factory
attribute tvb.simulator.models.zerlaut.ZerlautFirstOrder.state_variable_range = Final(field_type=<class 'dict'>, default={'E': array([0. , 0.1]), 'I': array([0. , 0.1]), 'W': array([ 0., 100.])}, required=True)
WARNING Field seems mutable and has a default value. Consider using a lambda as a value factory
attribute tvb.simulator.models.zerlaut.ZerlautSecondOrder.state_variable_range = Final(field_type=<class 'dict'>, default={'E': array([0. , 0.1]), 'I': array([0. , 0.1]), 'C_ee': array([0., 0.]), 'C_ei': array([0., 0.]), 'C_ii': array([0., 0.]), 'W': array([ 0., 100.])}, required=True)
WARNING Field seems mutable and has a default value. Consider using a lambda as a value factory
attribute tvb.datatypes.time_series.TimeSeries.labels_dimensions = Attr(field_type=<class 'dict'>, default={}, required=True)
WARNING Field seems mutable and has a default value. Consider using a lambda as a value factory
attribute tvb.datatypes.projections.ProjectionMatrix.conductances = Attr(field_type=<class 'dict'>, default={'air': 0.0, 'skin': 1.0, 'skull': 0.01, 'brain': 1.0}, required=False)
WARNING default contains values out of the declared domain. Ex 1.0
attribute tvb.simulator.coupling.HyperbolicTangent.b = NArray(label=':math:`b`', dtype=float64, default=array([1.]), dim_names=(), ndim=None, required=True)
WARNING default contains values out of the declared domain. Ex 1.0
attribute tvb.simulator.coupling.Kuramoto.a = NArray(label=':math:`a`', dtype=float64, default=array([1.]), dim_names=(), ndim=None, required=True)
Display the local connectivity kernel definining the local coupling strength for one focal point¶
When defining stimuli on the cortical surface, it's useful to visualize the spatial pattern being implemented:
Here, we'll redefine the local connectivity kernel,
In [2]:
# # configure local connectivity kernel
# loc_cortex = cortex.Cortex().from_file()
# loc_conn = local_connectivity.LocalConnectivity(cutoff=20.0, surface=loc_cortex.region_mapping_data.surface)
# loc_conn.equation.parameters['sigma'] = 10.0
# loc_conn.equation.parameters['amp'] = 1.0
# configure cortical surface
ctx = cortex.Cortex.from_file()
loc_conn = local_connectivity.LocalConnectivity(cutoff=20.0, surface=ctx.region_mapping_data.surface)
loc_conn.equation.parameters['sigma'] = 10.0
loc_conn.equation.parameters['amp'] = 1.0
ctx.local_connectivity = loc_conn
ctx.coupling_strength = numpy.array([0.0115])
ctx.configure()
# plot
figure()
ax = subplot(111, projection='3d')
x, y, z = ctx.vertices.T
ax.plot_trisurf(x, y, z, triangles=ctx.triangles, alpha=0.1, edgecolor='none')
Out[2]:
<mpl_toolkits.mplot3d.art3d.Poly3DCollection at 0x7efece9c3d10>
In [3]:
ctx
Out[3]:
| value | |
|---|---|
| Type | Cortex |
| coupling_strength [min, median, max] | [0.0115, 0.0115, 0.0115] |
| coupling_strength dtype | float64 |
| coupling_strength shape | (1,) |
| gid | UUID('6546b0e6-f1e5-43bc-a166-6b27d73ee67f') |
| local_connectivity | LocalConnectivity gid: 0b678ccd-a9b8-404d-a745-2447524ce643 |
| region_mapping_data | RegionMapping gid: ff33b2a8-3f52-43ad-90d7-7fc42bcdc2f2 |
| title | Cortex gid: 6546b0e6-f1e5-43bc-a166-6b27d73ee67f |
In [ ]: