Class: Integrator

Fixed-step or adaptive ODE integrator with TVB-specific extensions (noise, transient time, etc.). Inherits abs_tol, rel_tol from Solver. Overrides method default to ‘euler’.

URI: tvbo:Integrator

 classDiagram
    class Integrator
    click Integrator href "./Integrator.html"
      Solver <|-- Integrator
        click Solver href "./Solver.html"
      
      Integrator : abs_tol
        
          
    
        
        
        Integrator --> "0..1" Float : abs_tol
        click Float href "../http://www.w3.org/2001/XMLSchema#float.html"
    

        
      Integrator : block_size
        
          
    
        
        
        Integrator --> "0..1" Integer : block_size
        click Integer href "../http://www.w3.org/2001/XMLSchema#integer.html"
    

        
      Integrator : coupling_evaluation
        
          
    
        
        
        Integrator --> "0..1" CouplingStageEvaluation : coupling_evaluation
        click CouplingStageEvaluation href "../../enums/CouplingStageEvaluation.html"
    

        
      Integrator : delayed
        
          
    
        
        
        Integrator --> "0..1" Boolean : delayed
        click Boolean href "../http://www.w3.org/2001/XMLSchema#boolean.html"
    

        
      Integrator : description
        
          
    
        
        
        Integrator --> "0..1" String : description
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

        
      Integrator : differentiation
        
          
    
        
        
        Integrator --> "0..1" Differentiation : differentiation
        click Differentiation href "./Differentiation.html"
    

        
      Integrator : duration
        
          
    
        
        
        Integrator --> "0..1" Float : duration
        click Float href "../http://www.w3.org/2001/XMLSchema#float.html"
    

        
      Integrator : intermediate_expressions
        
          
    
        
        
        Integrator --> "*" DerivedVariable : intermediate_expressions
        click DerivedVariable href "./DerivedVariable.html"
    

        
      Integrator : method
        
          
    
        
        
        Integrator --> "0..1" String : method
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

        
      Integrator : noise
        
          
    
        
        
        Integrator --> "0..1" Noise : noise
        click Noise href "./Noise.html"
    

        
      Integrator : noise_draw
        
          
    
        
        
        Integrator --> "0..1" NoiseDraw : noise_draw
        click NoiseDraw href "../../enums/NoiseDraw.html"
    

        
      Integrator : number_of_stages
        
          
    
        
        
        Integrator --> "0..1" Integer : number_of_stages
        click Integer href "../http://www.w3.org/2001/XMLSchema#integer.html"
    

        
      Integrator : parameters
        
          
    
        
        
        Integrator --> "*" Parameter : parameters
        click Parameter href "./Parameter.html"
    

        
      Integrator : rel_tol
        
          
    
        
        
        Integrator --> "0..1" Float : rel_tol
        click Float href "../http://www.w3.org/2001/XMLSchema#float.html"
    

        
      Integrator : scipy_ode_base
        
          
    
        
        
        Integrator --> "0..1" Boolean : scipy_ode_base
        click Boolean href "../http://www.w3.org/2001/XMLSchema#boolean.html"
    

        
      Integrator : state_wise_sigma
        
          
    
        
        
        Integrator --> "*" Float : state_wise_sigma
        click Float href "../http://www.w3.org/2001/XMLSchema#float.html"
    

        
      Integrator : step_size
        
          
    
        
        
        Integrator --> "0..1" Float : step_size
        click Float href "../http://www.w3.org/2001/XMLSchema#float.html"
    

        
      Integrator : steps
        
          
    
        
        
        Integrator --> "0..1" Integer : steps
        click Integer href "../http://www.w3.org/2001/XMLSchema#integer.html"
    

        
      Integrator : time_unit
        
          
    
        
        
        Integrator --> "0..1" UnitEnum : time_unit
        click UnitEnum href "../../enums/UnitEnum.html"
    

        
      Integrator : transient_time
        
          
    
        
        
        Integrator --> "0..1" Float : transient_time
        click Float href "../http://www.w3.org/2001/XMLSchema#float.html"
    

        
      Integrator : unit
        
          
    
        
        
        Integrator --> "0..1" String : unit
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

        
      Integrator : update_expression
        
          
    
        
        
        Integrator --> "0..1" DerivedVariable : update_expression
        click DerivedVariable href "./DerivedVariable.html"

Inheritance

Class Properties

Property Value
Class URI tvbo:Integrator

Slots

Name Cardinality and Range Description Inheritance
time_unit 0..1
UnitEnum		 Unit of every time-valued number in this scope — the step size, any period, a… direct
unit 0..1
xsd:string or 
UnitEnum		 Physical unit of measurement direct
parameters *
Parameter		 direct
duration 0..1
xsd:float		 Length of the MEASURED window — what the run hands back direct
description 0..1
xsd:string		 direct
method 0..1
xsd:string		 Integration method (euler, heun, rk4, etc direct
step_size 0..1
xsd:float		 direct
steps 0..1
xsd:integer		 direct
noise 0..1
Noise		 direct
state_wise_sigma *
xsd:float		 direct
transient_time 0..1
xsd:float		 Length of the leading settling window, prepended to duration direct
block_size 0..1
xsd:integer		 Granularity of the nested block scan, in integration steps direct
noise_draw 0..1
NoiseDraw		 How the base solve draws its noise realization, and therefore WHICH realizati… direct
scipy_ode_base 0..1
xsd:boolean		 direct
number_of_stages 0..1
xsd:integer		 direct
intermediate_expressions *
DerivedVariable		 direct
update_expression 0..1
DerivedVariable		 direct
delayed 0..1
xsd:boolean		 direct
differentiation 0..1
Differentiation		 Backend-neutral strategy for propagating gradients through the temporal integ… direct
coupling_evaluation 0..1
CouplingStageEvaluation		 Backend-neutral numerical treatment of the network coupling term across the s… direct
abs_tol 0..1
xsd:float		 Absolute tolerance for adaptive solvers Solver
rel_tol 0..1
xsd:float		 Relative tolerance for adaptive solvers Solver

Usages

used by used in type used
Network integration range Integrator
Optimization integration range Integrator
Inference integration range Integrator
SimulationExperiment integration range Integrator

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/tvbo

Mappings

Mapping Type Mapped Value
self tvbo:Integrator
native tvbo:Integrator

LinkML Source

Direct

name: Integrator
description: Fixed-step or adaptive ODE integrator with TVB-specific extensions (noise,
  transient time, etc.). Inherits abs_tol, rel_tol from Solver. Overrides method default
  to 'euler'.
from_schema: https://w3id.org/tvbo
is_a: Solver
slots:
- time_unit
- unit
- parameters
- duration
- description
slot_usage:
  duration:
    name: duration
    description: Length of the MEASURED window — what the run hands back. Any `transient_time`
      is prepended to it, so total integrated time is `transient_time + duration`
      and raising the settle never shortens the data. Every backend measures this
      same window.
attributes:
  method:
    name: method
    description: Integration method (euler, heun, rk4, etc.)
    from_schema: https://w3id.org/tvbo
    ifabsent: string(euler)
    domain_of:
    - Discretization
    - InitialState
    - Solver
    - Integrator
    - PDESolver
    range: string
  step_size:
    name: step_size
    from_schema: https://w3id.org/tvbo
    aliases:
    - dt
    ifabsent: float(0.01220703125)
    domain_of:
    - Solver
    - Integrator
    range: float
  steps:
    name: steps
    from_schema: https://w3id.org/tvbo
    domain_of:
    - Procedure
    - Integrator
    range: integer
  noise:
    name: noise
    from_schema: https://w3id.org/tvbo
    domain_of:
    - Stimulus
    - StateVariable
    - Integrator
    range: Noise
    inlined: true
  state_wise_sigma:
    name: state_wise_sigma
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Integrator
    range: float
    multivalued: true
  transient_time:
    name: transient_time
    description: 'Length of the leading settling window, prepended to `duration`.
      It marks part of ONE integration — never a separate simulation: the backend
      integrates `transient_time + duration` in a single scan and the marked head
      is cut where the run is consumed (observations, analyses, plots, saved data),
      so the settle is in-band for any observation kernel that needs warm-up. Time
      is measured from the START of the measured window: the settle carries non-positive
      timestamps and ends at 0, the measured window opens one step later, and a declared
      event `t0` is relative to measurement, never to the scan. A settle that a fit
      reuses across many candidate evaluations is NOT this slot — that is a seed,
      declared as `initial_state.method: time_integration` with its own `duration`.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: float(0)
    domain_of:
    - Integrator
    range: float
  block_size:
    name: block_size
    description: 'Granularity of the nested block scan, in integration steps. Bounds
      the per-block memory so a streaming reduction folds an observable in-carry instead
      of materializing the trajectory. On a STOCHASTIC network this value is not a
      free tuning knob: with `noise_draw: blocked` the realization is a pure function
      of the noise key and the block index, so changing it changes the trajectory.
      Declare it and leave it alone.'
    from_schema: https://w3id.org/tvbo
    ifabsent: integer(1000)
    domain_of:
    - Exploration
    - Integrator
    range: integer
  noise_draw:
    name: noise_draw
    description: 'How the base solve draws its noise realization, and therefore WHICH
      realization it is: `fused` draws the whole [n_steps, ...] tensor in one call,
      `blocked` regenerates each block of `block_size` steps from (key, block_index).
      Those are different draws from the same seed, so the grain is a declared property
      of the integration rather than something inferred from how the run is consumed.
      An observable declared `reduce: streaming` folds block by block whatever this
      says, because a reduction has no trajectory to fold otherwise; declare `blocked`
      to put the whole run on that same grain.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: string(fused)
    domain_of:
    - Integrator
    range: NoiseDraw
  scipy_ode_base:
    name: scipy_ode_base
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: 'False'
    domain_of:
    - Integrator
    range: boolean
  number_of_stages:
    name: number_of_stages
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: integer(1)
    domain_of:
    - Integrator
    range: integer
  intermediate_expressions:
    name: intermediate_expressions
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Integrator
    range: DerivedVariable
    multivalued: true
    inlined: true
  update_expression:
    name: update_expression
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Integrator
    range: DerivedVariable
    inlined: true
  delayed:
    name: delayed
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: 'True'
    domain_of:
    - Integrator
    - Coupling
    range: boolean
  differentiation:
    name: differentiation
    description: Backend-neutral strategy for propagating gradients through the temporal
      integration (e.g. truncated backprop-through-time).
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Integrator
    range: Differentiation
    inlined: true
  coupling_evaluation:
    name: coupling_evaluation
    description: 'Backend-neutral numerical treatment of the network coupling term
      across the stages of a multi-stage integrator (Heun, RK4, ...): re-evaluated
      at every stage (per_stage — standard ODE accuracy) or computed once per step
      and held constant across stages (per_step — a TVB-style efficiency shortcut).
      Single- stage methods (Euler) and always-recompute solvers (diffrax) ignore
      it. per_stage is required to match reference integrators for stiff / chaotic
      / multistable systems, where the frozen- coupling error can select a different
      trajectory or attractor. See CouplingStageEvaluation.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: string(per_step)
    domain_of:
    - Integrator
    range: CouplingStageEvaluation
class_uri: tvbo:Integrator

Induced

name: Integrator
description: Fixed-step or adaptive ODE integrator with TVB-specific extensions (noise,
  transient time, etc.). Inherits abs_tol, rel_tol from Solver. Overrides method default
  to 'euler'.
from_schema: https://w3id.org/tvbo
is_a: Solver
slot_usage:
  duration:
    name: duration
    description: Length of the MEASURED window — what the run hands back. Any `transient_time`
      is prepended to it, so total integrated time is `transient_time + duration`
      and raising the settle never shortens the data. Every backend measures this
      same window.
attributes:
  method:
    name: method
    description: Integration method (euler, heun, rk4, etc.)
    from_schema: https://w3id.org/tvbo
    ifabsent: string(euler)
    owner: Integrator
    domain_of:
    - Discretization
    - InitialState
    - Solver
    - Integrator
    - PDESolver
    range: string
  step_size:
    name: step_size
    from_schema: https://w3id.org/tvbo
    aliases:
    - dt
    ifabsent: float(0.01220703125)
    owner: Integrator
    domain_of:
    - Solver
    - Integrator
    range: float
  steps:
    name: steps
    from_schema: https://w3id.org/tvbo
    owner: Integrator
    domain_of:
    - Procedure
    - Integrator
    range: integer
  noise:
    name: noise
    from_schema: https://w3id.org/tvbo
    owner: Integrator
    domain_of:
    - Stimulus
    - StateVariable
    - Integrator
    range: Noise
    inlined: true
  state_wise_sigma:
    name: state_wise_sigma
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Integrator
    domain_of:
    - Integrator
    range: float
    multivalued: true
  transient_time:
    name: transient_time
    description: 'Length of the leading settling window, prepended to `duration`.
      It marks part of ONE integration — never a separate simulation: the backend
      integrates `transient_time + duration` in a single scan and the marked head
      is cut where the run is consumed (observations, analyses, plots, saved data),
      so the settle is in-band for any observation kernel that needs warm-up. Time
      is measured from the START of the measured window: the settle carries non-positive
      timestamps and ends at 0, the measured window opens one step later, and a declared
      event `t0` is relative to measurement, never to the scan. A settle that a fit
      reuses across many candidate evaluations is NOT this slot — that is a seed,
      declared as `initial_state.method: time_integration` with its own `duration`.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: float(0)
    owner: Integrator
    domain_of:
    - Integrator
    range: float
  block_size:
    name: block_size
    description: 'Granularity of the nested block scan, in integration steps. Bounds
      the per-block memory so a streaming reduction folds an observable in-carry instead
      of materializing the trajectory. On a STOCHASTIC network this value is not a
      free tuning knob: with `noise_draw: blocked` the realization is a pure function
      of the noise key and the block index, so changing it changes the trajectory.
      Declare it and leave it alone.'
    from_schema: https://w3id.org/tvbo
    ifabsent: integer(1000)
    owner: Integrator
    domain_of:
    - Exploration
    - Integrator
    range: integer
  noise_draw:
    name: noise_draw
    description: 'How the base solve draws its noise realization, and therefore WHICH
      realization it is: `fused` draws the whole [n_steps, ...] tensor in one call,
      `blocked` regenerates each block of `block_size` steps from (key, block_index).
      Those are different draws from the same seed, so the grain is a declared property
      of the integration rather than something inferred from how the run is consumed.
      An observable declared `reduce: streaming` folds block by block whatever this
      says, because a reduction has no trajectory to fold otherwise; declare `blocked`
      to put the whole run on that same grain.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: string(fused)
    owner: Integrator
    domain_of:
    - Integrator
    range: NoiseDraw
  scipy_ode_base:
    name: scipy_ode_base
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: 'False'
    owner: Integrator
    domain_of:
    - Integrator
    range: boolean
  number_of_stages:
    name: number_of_stages
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: integer(1)
    owner: Integrator
    domain_of:
    - Integrator
    range: integer
  intermediate_expressions:
    name: intermediate_expressions
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Integrator
    domain_of:
    - Integrator
    range: DerivedVariable
    multivalued: true
    inlined: true
  update_expression:
    name: update_expression
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Integrator
    domain_of:
    - Integrator
    range: DerivedVariable
    inlined: true
  delayed:
    name: delayed
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: 'True'
    owner: Integrator
    domain_of:
    - Integrator
    - Coupling
    range: boolean
  differentiation:
    name: differentiation
    description: Backend-neutral strategy for propagating gradients through the temporal
      integration (e.g. truncated backprop-through-time).
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Integrator
    domain_of:
    - Integrator
    range: Differentiation
    inlined: true
  coupling_evaluation:
    name: coupling_evaluation
    description: 'Backend-neutral numerical treatment of the network coupling term
      across the stages of a multi-stage integrator (Heun, RK4, ...): re-evaluated
      at every stage (per_stage — standard ODE accuracy) or computed once per step
      and held constant across stages (per_step — a TVB-style efficiency shortcut).
      Single- stage methods (Euler) and always-recompute solvers (diffrax) ignore
      it. per_stage is required to match reference integrators for stiff / chaotic
      / multistable systems, where the frozen- coupling error can select a different
      trajectory or attractor. See CouplingStageEvaluation.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: string(per_step)
    owner: Integrator
    domain_of:
    - Integrator
    range: CouplingStageEvaluation
  time_unit:
    name: time_unit
    description: 'Unit of every time-valued number in this scope — the step size,
      any period, and the physical meaning of one model time-step. Declared at whichever
      scope owns the clock (network, integrator, observation); `tvbo.utils.units.time_unit_of`
      resolves a scope to its effective unit by walking outwards, and states the `ms`
      fallback once, at the end of that walk. Deliberately carries no default: a defaulted
      slot cannot be inherited through, so `ifabsent: ms` made an unset unit indistinguishable
      from one someone wrote, and masked an explicitly declared `s` one scope out.
      `time_scale` is accepted as a synonym.'
    from_schema: https://w3id.org/tvbo
    aliases:
    - time_scale
    rank: 1000
    owner: Integrator
    domain_of:
    - Network
    - Observation
    - Integrator
    range: UnitEnum
  unit:
    name: unit
    description: 'Physical unit of measurement. `UnitEnum` is the curated vocabulary
      — each of its values is vendored from QUDT (`ontology/tvb-o-units.ttl`) and
      can be reasoned about dimensionally. The range is deliberately open beyond it:
      a unit nobody has curated yet is recorded as written and reported `uncurated`,
      because a closed range forces the author to either misdeclare the quantity or
      leave it undeclared, and both lose more than an unrecognised string does. An
      uncurated unit carries no dimensional claim, so a check involving it reports
      `underdetermined` rather than guessing. Promote one with `tvbo units add <unit>`,
      which pulls its QUDT record into the vendored module — so every unit TVBO *reasons*
      about stays authoritative, and only what it *records* is open.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: qudt:unit
    owner: Integrator
    domain_of:
    - CommonCoordinateSpace
    - ToolUnit
    - MeasureSpec
    - NamedArray
    - Edge
    - Observation
    - StateVariable
    - Parameter
    - Argument
    - DerivedParameter
    - DerivedVariable
    - ExplorationAxis
    - Integrator
    - TimeSeries
    - NDArray
    - SpatialField
    range: string
    any_of:
    - range: UnitEnum
    - range: string
  parameters:
    name: parameters
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Integrator
    domain_of:
    - Equation
    - Stimulus
    - Event
    - ExperimentResultSidecar
    - Network
    - GraphGenerator
    - Node
    - Edge
    - Observation
    - Analysis
    - Dynamics
    - Distribution
    - Noise
    - Exploration
    - Discretization
    - BranchSwitch
    - Integrator
    - Coupling
    - PDE
    range: Parameter
    multivalued: true
    inlined: true
  duration:
    name: duration
    description: Length of the MEASURED window — what the run hands back. Any `transient_time`
      is prepended to it, so total integrated time is `transient_time + duration`
      and raising the settle never shortens the data. Every backend measures this
      same window.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: float(1000)
    owner: Integrator
    domain_of:
    - Stimulus
    - Event
    - InitialState
    - Integrator
    range: float
  description:
    name: description
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: dcterms:description
    owner: Integrator
    domain_of:
    - CommonCoordinateSpace
    - Dataset
    - StudyLayout
    - StudyTemplate
    - StudyDirectory
    - StudyFile
    - ClinicalScore
    - SoftwarePackage
    - SoftwareRequirement
    - SoftwareEnvironment
    - Figure
    - Panel
    - Equation
    - Stimulus
    - Event
    - Tractogram
    - Matrix
    - ResultEntity
    - Activity
    - Phenotype
    - MeasureSpec
    - NamedArray
    - Network
    - GraphGenerator
    - ProcedureStep
    - File
    - Node
    - Edge
    - Observation
    - Dynamics
    - StateVariable
    - Parameter
    - CouplingInput
    - Argument
    - Function
    - FunctionCall
    - Callable
    - DerivedParameter
    - DerivedVariable
    - RandomStream
    - DataSource
    - OptimizationStage
    - Exploration
    - ExplorationAxis
    - FreeParameter
    - Inference
    - Prior
    - Likelihood
    - UpdateRule
    - AlgorithmStage
    - TuningObjective
    - Algorithm
    - BranchSwitch
    - Continuation
    - Integrator
    - Coupling
    - RegionMapping
    - SimulationExperiment
    - Study
    - ResultBinding
    - TimeSeries
    - NDArray
    - SpatialDomain
    - Mesh
    - SpatialField
    - FieldStateVariable
    - BoundaryCondition
    - PDESolver
    - PDE
    - Reducer
    range: string
  abs_tol:
    name: abs_tol
    description: Absolute tolerance for adaptive solvers.
    from_schema: https://w3id.org/tvbo
    ifabsent: float(1e-10)
    owner: Integrator
    domain_of:
    - InitialState
    - Solver
    range: float
  rel_tol:
    name: rel_tol
    description: Relative tolerance for adaptive solvers.
    from_schema: https://w3id.org/tvbo
    ifabsent: float(1e-10)
    owner: Integrator
    domain_of:
    - InitialState
    - Solver
    range: float
class_uri: tvbo:Integrator