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simulator Package

coupling_forms

class tvb.adapters.simulator.coupling_forms.DifferenceCouplingForm(prefix='')[source]

Bases: tvb.adapters.simulator.form_with_ranges.FormWithRanges

class tvb.adapters.simulator.coupling_forms.HyperbolicTangentCouplingForm(prefix='')[source]

Bases: tvb.adapters.simulator.form_with_ranges.FormWithRanges

class tvb.adapters.simulator.coupling_forms.KuramotoCouplingForm(prefix='')[source]

Bases: tvb.adapters.simulator.form_with_ranges.FormWithRanges

class tvb.adapters.simulator.coupling_forms.LinearCouplingForm(prefix='')[source]

Bases: tvb.adapters.simulator.form_with_ranges.FormWithRanges

class tvb.adapters.simulator.coupling_forms.PreSigmoidalCouplingForm(prefix='')[source]

Bases: tvb.adapters.simulator.form_with_ranges.FormWithRanges

class tvb.adapters.simulator.coupling_forms.ScalingCouplingForm(prefix='')[source]

Bases: tvb.adapters.simulator.form_with_ranges.FormWithRanges

class tvb.adapters.simulator.coupling_forms.SigmoidalCouplingForm(prefix='')[source]

Bases: tvb.adapters.simulator.form_with_ranges.FormWithRanges

class tvb.adapters.simulator.coupling_forms.SigmoidalJansenRitForm(prefix='')[source]

Bases: tvb.adapters.simulator.form_with_ranges.FormWithRanges

tvb.adapters.simulator.coupling_forms.get_coupling_to_form_dict()[source]
tvb.adapters.simulator.coupling_forms.get_form_for_coupling(coupling_class)[source]
tvb.adapters.simulator.coupling_forms.get_ui_name_to_coupling_dict()[source]

equation_forms

class tvb.adapters.simulator.equation_forms.AlphaEquationForm(prefix='')[source]

Bases: tvb.adapters.simulator.equation_forms.EquationForm

fill_trait(datatype)[source]
get_traited_equation()[source]
class tvb.adapters.simulator.equation_forms.CosineEquationForm(prefix='')[source]

Bases: tvb.adapters.simulator.equation_forms.EquationForm

fill_trait(datatype)[source]
get_traited_equation()[source]
class tvb.adapters.simulator.equation_forms.DoubleExponentialEquationForm(prefix='')[source]

Bases: tvb.adapters.simulator.equation_forms.EquationForm

fill_trait(datatype)[source]
get_traited_equation()[source]
class tvb.adapters.simulator.equation_forms.DoubleGaussianEquationForm(prefix='')[source]

Bases: tvb.adapters.simulator.equation_forms.EquationForm

fill_trait(datatype)[source]
get_traited_equation()[source]
class tvb.adapters.simulator.equation_forms.EquationForm(prefix='')[source]

Bases: tvb.core.neotraits.forms.Form

get_traited_equation()[source]
class tvb.adapters.simulator.equation_forms.FirstOrderVolterraEquationForm(prefix='')[source]

Bases: tvb.adapters.simulator.equation_forms.EquationForm

fill_trait(datatype)[source]
get_traited_equation()[source]
class tvb.adapters.simulator.equation_forms.GammaEquationForm(prefix='')[source]

Bases: tvb.adapters.simulator.equation_forms.EquationForm

fill_trait(datatype)[source]
get_traited_equation()[source]
class tvb.adapters.simulator.equation_forms.GaussianEquationForm(prefix='')[source]

Bases: tvb.adapters.simulator.equation_forms.EquationForm

fill_trait(datatype)[source]
get_traited_equation()[source]
class tvb.adapters.simulator.equation_forms.GeneralizedSigmoidEquationForm(prefix='')[source]

Bases: tvb.adapters.simulator.equation_forms.EquationForm

fill_trait(datatype)[source]
get_traited_equation()[source]
class tvb.adapters.simulator.equation_forms.LinearEquationForm(prefix='')[source]

Bases: tvb.adapters.simulator.equation_forms.EquationForm

fill_trait(datatype)[source]
get_traited_equation()[source]
class tvb.adapters.simulator.equation_forms.MixtureOfGammasEquationForm(prefix='')[source]

Bases: tvb.adapters.simulator.equation_forms.EquationForm

fill_trait(datatype)[source]
get_traited_equation()[source]
class tvb.adapters.simulator.equation_forms.PulseTrainEquationForm(prefix='')[source]

Bases: tvb.adapters.simulator.equation_forms.EquationForm

fill_trait(datatype)[source]
get_traited_equation()[source]
class tvb.adapters.simulator.equation_forms.SigmoidEquationForm(prefix='')[source]

Bases: tvb.adapters.simulator.equation_forms.EquationForm

fill_trait(datatype)[source]
get_traited_equation()[source]
class tvb.adapters.simulator.equation_forms.SinusoidEquationForm(prefix='')[source]

Bases: tvb.adapters.simulator.equation_forms.EquationForm

fill_trait(datatype)[source]
get_traited_equation()[source]
tvb.adapters.simulator.equation_forms.get_equation_to_form_dict()[source]
tvb.adapters.simulator.equation_forms.get_form_for_equation(equation_class)[source]
tvb.adapters.simulator.equation_forms.get_ui_name_to_equation_dict()[source]
tvb.adapters.simulator.equation_forms.get_ui_name_to_monitor_equation_dict()[source]

form_with_ranges

class tvb.adapters.simulator.form_with_ranges.FormWithRanges(prefix='', project_id=None, draw_ranges=True)[source]

Bases: tvb.core.neotraits.forms.Form

get_range_parameters()[source]

integrator_forms

class tvb.adapters.simulator.integrator_forms.Dop853IntegratorForm(prefix='')[source]

Bases: tvb.adapters.simulator.integrator_forms.IntegratorForm

class tvb.adapters.simulator.integrator_forms.Dop853StochasticIntegratorForm(prefix='')[source]

Bases: tvb.adapters.simulator.integrator_forms.IntegratorStochasticForm

class tvb.adapters.simulator.integrator_forms.Dopri5IntegratorForm(prefix='')[source]

Bases: tvb.adapters.simulator.integrator_forms.IntegratorForm

class tvb.adapters.simulator.integrator_forms.Dopri5StochasticIntegratorForm(prefix='')[source]

Bases: tvb.adapters.simulator.integrator_forms.IntegratorStochasticForm

class tvb.adapters.simulator.integrator_forms.EulerDeterministicIntegratorForm(prefix='')[source]

Bases: tvb.adapters.simulator.integrator_forms.IntegratorForm

class tvb.adapters.simulator.integrator_forms.EulerStochasticIntegratorForm(prefix='')[source]

Bases: tvb.adapters.simulator.integrator_forms.IntegratorStochasticForm

class tvb.adapters.simulator.integrator_forms.HeunDeterministicIntegratorForm(prefix='')[source]

Bases: tvb.adapters.simulator.integrator_forms.IntegratorForm

class tvb.adapters.simulator.integrator_forms.HeunStochasticIntegratorForm(prefix='')[source]

Bases: tvb.adapters.simulator.integrator_forms.IntegratorStochasticForm

class tvb.adapters.simulator.integrator_forms.IdentityIntegratorForm(prefix='')[source]

Bases: tvb.adapters.simulator.integrator_forms.IntegratorForm

class tvb.adapters.simulator.integrator_forms.IntegratorForm(prefix='')[source]

Bases: tvb.core.neotraits.forms.Form

class tvb.adapters.simulator.integrator_forms.IntegratorStochasticForm(prefix='')[source]

Bases: tvb.adapters.simulator.integrator_forms.IntegratorForm

fill_from_trait(trait)[source]
fill_trait(datatype)[source]
template = 'select_field.jinja2'
class tvb.adapters.simulator.integrator_forms.RungeKutta4thOrderDeterministicIntegratorForm(prefix='')[source]

Bases: tvb.adapters.simulator.integrator_forms.IntegratorForm

class tvb.adapters.simulator.integrator_forms.VODEIntegratorForm(prefix='')[source]

Bases: tvb.adapters.simulator.integrator_forms.IntegratorForm

class tvb.adapters.simulator.integrator_forms.VODEStochasticIntegratorForm(prefix='')[source]

Bases: tvb.adapters.simulator.integrator_forms.IntegratorStochasticForm

tvb.adapters.simulator.integrator_forms.get_form_for_integrator(integrator_class)[source]
tvb.adapters.simulator.integrator_forms.get_integrator_to_form_dict()[source]
tvb.adapters.simulator.integrator_forms.get_ui_name_to_integrator_dict()[source]

model_forms

class tvb.adapters.simulator.model_forms.Epileptor2DModelForm(prefix='')[source]

Bases: tvb.adapters.simulator.form_with_ranges.FormWithRanges

class tvb.adapters.simulator.model_forms.EpileptorCodim3ModelForm(prefix='')[source]

Bases: tvb.adapters.simulator.form_with_ranges.FormWithRanges

class tvb.adapters.simulator.model_forms.EpileptorCodim3SlowModModelForm(prefix='')[source]

Bases: tvb.adapters.simulator.form_with_ranges.FormWithRanges

class tvb.adapters.simulator.model_forms.EpileptorModelForm(prefix='')[source]

Bases: tvb.adapters.simulator.form_with_ranges.FormWithRanges

class tvb.adapters.simulator.model_forms.EpileptorRestingStateModelForm(prefix='')[source]

Bases: tvb.adapters.simulator.form_with_ranges.FormWithRanges

class tvb.adapters.simulator.model_forms.Generic2dOscillatorModelForm(prefix='')[source]

Bases: tvb.adapters.simulator.form_with_ranges.FormWithRanges

class tvb.adapters.simulator.model_forms.HopfieldModelForm(prefix='')[source]

Bases: tvb.adapters.simulator.form_with_ranges.FormWithRanges

class tvb.adapters.simulator.model_forms.JansenRitModelForm(prefix='')[source]

Bases: tvb.adapters.simulator.form_with_ranges.FormWithRanges

class tvb.adapters.simulator.model_forms.KuramotoModelForm(prefix='')[source]

Bases: tvb.adapters.simulator.form_with_ranges.FormWithRanges

class tvb.adapters.simulator.model_forms.LarterBreakspearModelForm(prefix='')[source]

Bases: tvb.adapters.simulator.form_with_ranges.FormWithRanges

class tvb.adapters.simulator.model_forms.LinearModelForm(prefix='')[source]

Bases: tvb.adapters.simulator.form_with_ranges.FormWithRanges

class tvb.adapters.simulator.model_forms.ReducedSetFitzHughNagumoModelForm(prefix='')[source]

Bases: tvb.adapters.simulator.form_with_ranges.FormWithRanges

class tvb.adapters.simulator.model_forms.ReducedSetHindmarshRoseModelForm(prefix='')[source]

Bases: tvb.adapters.simulator.form_with_ranges.FormWithRanges

class tvb.adapters.simulator.model_forms.ReducedWongWangExcInhModelForm(prefix='')[source]

Bases: tvb.adapters.simulator.form_with_ranges.FormWithRanges

class tvb.adapters.simulator.model_forms.ReducedWongWangModelForm(prefix='')[source]

Bases: tvb.adapters.simulator.form_with_ranges.FormWithRanges

class tvb.adapters.simulator.model_forms.StateVariableRangesForm(prefix='')[source]

Bases: tvb.core.neotraits.forms.Form

class tvb.adapters.simulator.model_forms.SupHopfModelForm(prefix='')[source]

Bases: tvb.adapters.simulator.form_with_ranges.FormWithRanges

class tvb.adapters.simulator.model_forms.WilsonCowanModelForm(prefix='')[source]

Bases: tvb.adapters.simulator.form_with_ranges.FormWithRanges

class tvb.adapters.simulator.model_forms.ZerlautFirstOrderModelForm(prefix='')[source]

Bases: tvb.adapters.simulator.form_with_ranges.FormWithRanges

class tvb.adapters.simulator.model_forms.ZerlautSecondOrderModelForm(prefix='')[source]

Bases: tvb.adapters.simulator.model_forms.ZerlautFirstOrderModelForm

class tvb.adapters.simulator.model_forms.ZetterbergJansenModelForm(prefix='')[source]

Bases: tvb.adapters.simulator.form_with_ranges.FormWithRanges

tvb.adapters.simulator.model_forms.get_form_for_model(model_class)[source]
tvb.adapters.simulator.model_forms.get_model_to_form_dict()[source]
tvb.adapters.simulator.model_forms.get_ui_name_to_model()[source]

monitor_forms

class tvb.adapters.simulator.monitor_forms.BoldMonitorForm(prefix='', project_id=None)[source]

Bases: tvb.adapters.simulator.monitor_forms.MonitorForm

fill_trait(datatype)[source]
class tvb.adapters.simulator.monitor_forms.BoldRegionROIMonitorForm(prefix='', project_id=None)[source]

Bases: tvb.adapters.simulator.monitor_forms.BoldMonitorForm

class tvb.adapters.simulator.monitor_forms.EEGMonitorForm(prefix='', project_id=None)[source]

Bases: tvb.adapters.simulator.monitor_forms.ProjectionMonitorForm

class tvb.adapters.simulator.monitor_forms.GlobalAverageMonitorForm(prefix='', project_id=None)[source]

Bases: tvb.adapters.simulator.monitor_forms.MonitorForm

class tvb.adapters.simulator.monitor_forms.MEGMonitorForm(prefix='', project_id=None)[source]

Bases: tvb.adapters.simulator.monitor_forms.ProjectionMonitorForm

class tvb.adapters.simulator.monitor_forms.MonitorForm(prefix='', project_id=None)[source]

Bases: tvb.core.neotraits.forms.Form

class tvb.adapters.simulator.monitor_forms.ProjectionMonitorForm(prefix='', project_id=None)[source]

Bases: tvb.adapters.simulator.monitor_forms.MonitorForm

class tvb.adapters.simulator.monitor_forms.RawMonitorForm(prefix='', project_id=None)[source]

Bases: tvb.adapters.simulator.monitor_forms.MonitorForm

class tvb.adapters.simulator.monitor_forms.SpatialAverageMonitorForm(prefix='', project_id=None)[source]

Bases: tvb.adapters.simulator.monitor_forms.MonitorForm

class tvb.adapters.simulator.monitor_forms.SubSampleMonitorForm(prefix='', project_id=None)[source]

Bases: tvb.adapters.simulator.monitor_forms.MonitorForm

class tvb.adapters.simulator.monitor_forms.TemporalAverageMonitorForm(prefix='', project_id=None)[source]

Bases: tvb.core.neotraits.forms.Form

tvb.adapters.simulator.monitor_forms.get_form_for_monitor(monitor_class)[source]
tvb.adapters.simulator.monitor_forms.get_monitor_to_form_dict()[source]
tvb.adapters.simulator.monitor_forms.get_ui_name_to_monitor_dict()[source]
class tvb.adapters.simulator.monitor_forms.iEEGMonitorForm(prefix='', project_id=None)[source]

Bases: tvb.adapters.simulator.monitor_forms.ProjectionMonitorForm

noise_forms

class tvb.adapters.simulator.noise_forms.AdditiveNoiseForm(prefix='')[source]

Bases: tvb.adapters.simulator.noise_forms.NoiseForm

fill_from_trait(trait)[source]
get_range_parameters()[source]
class tvb.adapters.simulator.noise_forms.MultiplicativeNoiseForm(prefix='')[source]

Bases: tvb.adapters.simulator.noise_forms.NoiseForm

fill_trait(datatype)[source]
class tvb.adapters.simulator.noise_forms.NoiseForm(prefix='')[source]

Bases: tvb.adapters.simulator.form_with_ranges.FormWithRanges

fill_from_trait(trait)[source]
tvb.adapters.simulator.noise_forms.get_form_for_noise(noise_class)[source]
tvb.adapters.simulator.noise_forms.get_ui_name_to_noise_dict()[source]

range_parameter

class tvb.adapters.simulator.range_parameter.RangeParameter(name, type, range_definition, is_array=False)[source]

Bases: builtins.object

static from_json(range_json)[source]
get_range_values()[source]
to_json()[source]
class tvb.adapters.simulator.range_parameter.SimulatorRangeParameters(connectivity_filters=None, surface_filters=None, coupling=None, model=None, integrator_noise=None)[source]

Bases: builtins.object

add_connectivity_filter(filter)[source]
add_surface_filter(filter)[source]
get_all_range_parameters()[source]

simulate_algorithm_category_config

simulator_adapter

Adapter that uses the traits module to generate interfaces to the Simulator. Few supplementary steps are done here:

  • from submitted Monitor/Model... names, build transient entities
  • after UI parameters submit, compose transient Cortex entity to be passed to the Simulator.
class tvb.adapters.simulator.simulator_adapter.SimulatorAdapter[source]

Bases: tvb.core.adapters.abcadapter.ABCAsynchronous

Interface between the Simulator and the Framework.

HAVE_STATE_VARIABLES = ['GlobalAverage', 'SpatialAverage', 'Raw', 'SubSample', 'TemporalAverage']
algorithm = None
branch_simulation_state_gid = None
configure(simulator_gid)[source]

Make preparations for the adapter launch.

get_execution_time_approximation(**kwargs)[source]

Method should approximate based on input arguments, the time it will take for the operation to finish (in seconds).

get_form_class()[source]
get_output()[source]
Returns:list of classes for possible results of the Simulator.
get_required_disk_size(**kwargs)[source]

Return the required disk size this algorithm estimates it will take. (in kB)

get_required_memory_size(**kwargs)[source]

Return the required memory to run this algorithm.

launch(simulator_gid)[source]
Called from the GUI to launch a simulation.
: string class name of chosen model, etc... *_parameters: dictionary of parameters for chosen model, etc... connectivity: tvb.datatypes.connectivity.Connectivity object. surface: tvb.datatypes.surfaces.CorticalSurface: or None. stimulus: tvb.datatypes.patters. object
class tvb.adapters.simulator.simulator_adapter.SimulatorAdapterForm(prefix='', project_id=None, is_copy=False)[source]

Bases: tvb.core.adapters.abcadapter.ABCAdapterForm

fill_from_trait(trait)[source]
static get_filters()[source]
static get_input_name()[source]
static get_required_datatype()[source]
get_traited_datatype()[source]

simulator_fragments

class tvb.adapters.simulator.simulator_fragments.SimulatorFinalFragment(prefix='', project_id=None)[source]

Bases: tvb.core.adapters.abcadapter.ABCAdapterForm

fill_from_post(form_data)[source]
static is_burst_name_ok(burst_name)[source]
class tvb.adapters.simulator.simulator_fragments.SimulatorIntegratorFragment(prefix='', project_id=None)[source]

Bases: tvb.core.adapters.abcadapter.ABCAdapterForm

fill_from_trait(trait)[source]
class tvb.adapters.simulator.simulator_fragments.SimulatorLengthFragment(prefix='', project_id=None)[source]

Bases: tvb.core.adapters.abcadapter.ABCAdapterForm

class tvb.adapters.simulator.simulator_fragments.SimulatorModelFragment(prefix='', project_id=None)[source]

Bases: tvb.core.adapters.abcadapter.ABCAdapterForm

fill_from_trait(trait)[source]
class tvb.adapters.simulator.simulator_fragments.SimulatorMonitorFragment(prefix='', project_id=None)[source]

Bases: tvb.core.adapters.abcadapter.ABCAdapterForm

fill_from_trait(trait)[source]
class tvb.adapters.simulator.simulator_fragments.SimulatorPSEConfigurationFragment(choices, prefix='', project_id=None)[source]

Bases: tvb.core.adapters.abcadapter.ABCAdapterForm

class tvb.adapters.simulator.simulator_fragments.SimulatorPSEParamRangeFragment(pse_param1, pse_param2, prefix='', project_id=None)[source]

Bases: tvb.core.adapters.abcadapter.ABCAdapterForm

static fill_from_post(all_range_parameters, **data)[source]
class tvb.adapters.simulator.simulator_fragments.SimulatorRMFragment(prefix='', project_id=None, surface_index=None)[source]

Bases: tvb.core.adapters.abcadapter.ABCAdapterForm

fill_from_trait(trait)[source]
class tvb.adapters.simulator.simulator_fragments.SimulatorStimulusFragment(prefix='', project_id=None, is_surface_simulation=False)[source]

Bases: tvb.core.adapters.abcadapter.ABCAdapterForm

fill_from_trait(trait)[source]
class tvb.adapters.simulator.simulator_fragments.SimulatorSurfaceFragment(prefix='', project_id=None)[source]

Bases: tvb.core.adapters.abcadapter.ABCAdapterForm

fill_from_trait(trait)[source]