Connectivity normalization¶
With significant variability between methods of obtaining structural connectivity, it is often useful to normalize, in one sense or another, the connectivity when comparing, for example, across subjects, or standardizing parameter ranges.
In [1]:
%pylab nbagg
from tvb.simulator.lab import connectivity , plot_connectivity
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)
In [2]:
conn = connectivity.Connectivity.from_file()
conn.configure()
def plot_with_weights(weights):
conn = connectivity.Connectivity.from_file()
conn.configure()
conn.weights = weights
plot_connectivity(conn, num="tract_mode", plot_tracts=False)
plot_with_weights(conn.scaled_weights(mode='tract'))
WARNING File 'hemispheres' not found in ZIP. WARNING File 'hemispheres' not found in ZIP.
In [3]:
plot_with_weights(conn.scaled_weights(mode='region'))
plot_with_weights(conn.scaled_weights(mode='none'))
plot_with_weights(conn.transform_binarize_matrix())
plot_with_weights(conn.transform_remove_self_connections())
WARNING File 'hemispheres' not found in ZIP.
WARNING File 'hemispheres' not found in ZIP.
WARNING File 'hemispheres' not found in ZIP.
WARNING File 'hemispheres' not found in ZIP.
In [ ]: