Reference·Classes

Class: ProcedureStep

A single named step (or output) in a Procedure: one typed operation producing one named intermediate.

type selects the operation and therefore which of the fields below apply; it defaults to equation, the general case, so a Procedure written purely as equations needs no type annotations. The remaining fields carry each operation’s options as metadata rather than as call syntax, which is what lets a step lower directly to a backend-native primitive: expression parsing cannot represent keyword arguments at all, so any option written as one would be unresolvable.

URI: tvbo:ProcedureStep

 classDiagram
    class ProcedureStep
    click ProcedureStep href "./ProcedureStep.html"
      ProcedureStep : axis
        
          
    
        
        
        ProcedureStep --> "0..1" Integer : axis
        click Integer href "../http://www.w3.org/2001/XMLSchema#integer.html"
    

        
      ProcedureStep : comparison
        
          
    
        
        
        ProcedureStep --> "0..1" ComparisonOperator : comparison
        click ComparisonOperator href "../../enums/ComparisonOperator.html"
    

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

        
      ProcedureStep : diagonal
        
          
    
        
        
        ProcedureStep --> "0..1" ScalarValue : diagonal
        click ScalarValue href "./ScalarValue.html"
    

        
      ProcedureStep : distribution
        
          
    
        
        
        ProcedureStep --> "0..1" Distribution : distribution
        click Distribution href "./Distribution.html"
    

        
      ProcedureStep : equation
        
          
    
        
        
        ProcedureStep --> "0..1" Equation : equation
        click Equation href "./Equation.html"
    

        
      ProcedureStep : name
        
          
    
        
        
        ProcedureStep --> "1" String : name
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

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

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

        
      ProcedureStep : target_range
        
          
    
        
        
        ProcedureStep --> "0..1" Range : target_range
        click Range href "./Range.html"
    

        
      ProcedureStep : type
        
          
    
        
        
        ProcedureStep --> "0..1" ProcedureStepType : type
        click ProcedureStepType href "../../enums/ProcedureStepType.html"
    

        
      

Class Properties

Property	Value
Class URI	tvbo:ProcedureStep

Slots

Name	Cardinality and Range	Description	Inheritance
name	1 xsd:string	Globally unique identifier for the entity	direct
description	0..1 xsd:string		direct
type	0..1 ProcedureStepType	Which operation this step performs	direct
equation	0..1 Equation	The equation defining this step/output	direct
of	0..1 xsd:string	Name of the input this step consumes — the positions for pairwise_distance …	direct
axis	0..1 xsd:integer	Array axis a normalize step reduces over (0 = columns)	direct
diagonal	0..1 ScalarValue	Value written onto the diagonal of a pairwise_distance result, e	direct
distribution	0..1 Distribution	Distribution sampled by a sample / stochastic_mask step, or whose density…	direct
comparison	0..1 ComparisonOperator	Comparison a stochastic_mask applies between of and the draw	direct
seed_offset	0..1 xsd:integer	Sub-stream this step draws from, offset from the generator’s seed	direct
target_range	0..1 Range	Target interval for a minmax_rescale step (e	direct

Usages

used by	used in	type	used
Procedure	steps	range	ProcedureStep
Procedure	output	range	ProcedureStep

Identifier and Mapping Information

Schema Source

• from schema: https://w3id.org/tvbo

Mappings

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

LinkML Source

Direct

name: ProcedureStep
description: 'A single named step (or output) in a Procedure: one typed operation
  producing one named intermediate.

  `type` selects the operation and therefore which of the fields below apply; it defaults
  to `equation`, the general case, so a Procedure written purely as equations needs
  no type annotations. The remaining fields carry each operation''s options as *metadata*
  rather than as call syntax, which is what lets a step lower directly to a backend-native
  primitive: expression parsing cannot represent keyword arguments at all, so any
  option written as one would be unresolvable.'
from_schema: https://w3id.org/tvbo
slots:
- name
- description
attributes:
  type:
    name: type
    description: Which operation this step performs. Defaults to `equation`.
    from_schema: https://w3id.org/tvbo
    ifabsent: string(equation)
    domain_of:
    - Activity
    - GraphGenerator
    - ProcedureStep
    - File
    - Analysis
    - Aggregation
    - TuningObjective
    - Algorithm
    - Study
    range: ProcedureStepType
  equation:
    name: equation
    description: The equation defining this step/output. Used by `equation` steps
      (and by every output expression).
    from_schema: https://w3id.org/tvbo
    domain_of:
    - Stimulus
    - Event
    - ProcedureStep
    - Observation
    - StateVariable
    - Parameter
    - Function
    - FunctionCall
    - DerivedParameter
    - DerivedVariable
    - Noise
    - UpdateRule
    - DifferentialOperator
    - BoundaryCondition
    range: Equation
    inlined: true
  of:
    name: of
    description: Name of the input this step consumes — the positions for `pairwise_distance`
      / `distribution_pdf`, the matrix for `normalize`, the compared quantity for
      `stochastic_mask`, and for `sample` (which consumes no array) the Distribution-valued
      generator parameter to draw from. It names either a previously defined step
      or a generator parameter; steps are ordered, so a referenced step must already
      be defined.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - ProcedureStep
    range: string
  axis:
    name: axis
    description: Array axis a `normalize` step reduces over (0 = columns).
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - ProcedureStep
    - Distribution
    range: integer
  diagonal:
    name: diagonal
    description: Value written onto the diagonal of a `pairwise_distance` result,
      e.g. infinity to suppress self-connections. Omitted leaves the true zero self-distance
      in place.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - ProcedureStep
    range: ScalarValue
  distribution:
    name: distribution
    description: Distribution sampled by a `sample` / `stochastic_mask` step, or whose
      density a `distribution_pdf` step evaluates. Reuses the Distribution class,
      so a generator's randomness is declared exactly like any other sampled quantity
      in TVBO. On a `sample` step it is the family the generator defaults to, which
      the parameter named by `of` overrides when one is supplied.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - ProcedureStep
    - StateVariable
    - Parameter
    - Noise
    - Prior
    - Coupling
    range: Distribution
    inlined: true
  comparison:
    name: comparison
    description: Comparison a `stochastic_mask` applies between `of` and the draw.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: string(le)
    domain_of:
    - ProcedureStep
    range: ComparisonOperator
  seed_offset:
    name: seed_offset
    description: Sub-stream this step draws from, offset from the generator's seed.
      Two seeded steps must use different offsets to be independent. Stated here rather
      than inferred from step order so it is a property of the generator that every
      backend derives identically (numpy re-seeds, jax folds the offset into the key)
      — and so inserting or reordering steps cannot silently change an existing generator's
      output.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: int(0)
    domain_of:
    - ProcedureStep
    range: integer
  target_range:
    name: target_range
    description: Target interval for a `minmax_rescale` step (e.g. lo -1, hi 1).
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - ProcedureStep
    range: Range
    inlined: true
class_uri: tvbo:ProcedureStep

Induced

name: ProcedureStep
description: 'A single named step (or output) in a Procedure: one typed operation
  producing one named intermediate.

  `type` selects the operation and therefore which of the fields below apply; it defaults
  to `equation`, the general case, so a Procedure written purely as equations needs
  no type annotations. The remaining fields carry each operation''s options as *metadata*
  rather than as call syntax, which is what lets a step lower directly to a backend-native
  primitive: expression parsing cannot represent keyword arguments at all, so any
  option written as one would be unresolvable.'
from_schema: https://w3id.org/tvbo
attributes:
  type:
    name: type
    description: Which operation this step performs. Defaults to `equation`.
    from_schema: https://w3id.org/tvbo
    ifabsent: string(equation)
    owner: ProcedureStep
    domain_of:
    - Activity
    - GraphGenerator
    - ProcedureStep
    - File
    - Analysis
    - Aggregation
    - TuningObjective
    - Algorithm
    - Study
    range: ProcedureStepType
  equation:
    name: equation
    description: The equation defining this step/output. Used by `equation` steps
      (and by every output expression).
    from_schema: https://w3id.org/tvbo
    owner: ProcedureStep
    domain_of:
    - Stimulus
    - Event
    - ProcedureStep
    - Observation
    - StateVariable
    - Parameter
    - Function
    - FunctionCall
    - DerivedParameter
    - DerivedVariable
    - Noise
    - UpdateRule
    - DifferentialOperator
    - BoundaryCondition
    range: Equation
    inlined: true
  of:
    name: of
    description: Name of the input this step consumes — the positions for `pairwise_distance`
      / `distribution_pdf`, the matrix for `normalize`, the compared quantity for
      `stochastic_mask`, and for `sample` (which consumes no array) the Distribution-valued
      generator parameter to draw from. It names either a previously defined step
      or a generator parameter; steps are ordered, so a referenced step must already
      be defined.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: ProcedureStep
    domain_of:
    - ProcedureStep
    range: string
  axis:
    name: axis
    description: Array axis a `normalize` step reduces over (0 = columns).
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: ProcedureStep
    domain_of:
    - ProcedureStep
    - Distribution
    range: integer
  diagonal:
    name: diagonal
    description: Value written onto the diagonal of a `pairwise_distance` result,
      e.g. infinity to suppress self-connections. Omitted leaves the true zero self-distance
      in place.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: ProcedureStep
    domain_of:
    - ProcedureStep
    range: ScalarValue
  distribution:
    name: distribution
    description: Distribution sampled by a `sample` / `stochastic_mask` step, or whose
      density a `distribution_pdf` step evaluates. Reuses the Distribution class,
      so a generator's randomness is declared exactly like any other sampled quantity
      in TVBO. On a `sample` step it is the family the generator defaults to, which
      the parameter named by `of` overrides when one is supplied.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: ProcedureStep
    domain_of:
    - ProcedureStep
    - StateVariable
    - Parameter
    - Noise
    - Prior
    - Coupling
    range: Distribution
    inlined: true
  comparison:
    name: comparison
    description: Comparison a `stochastic_mask` applies between `of` and the draw.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: string(le)
    owner: ProcedureStep
    domain_of:
    - ProcedureStep
    range: ComparisonOperator
  seed_offset:
    name: seed_offset
    description: Sub-stream this step draws from, offset from the generator's seed.
      Two seeded steps must use different offsets to be independent. Stated here rather
      than inferred from step order so it is a property of the generator that every
      backend derives identically (numpy re-seeds, jax folds the offset into the key)
      — and so inserting or reordering steps cannot silently change an existing generator's
      output.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: int(0)
    owner: ProcedureStep
    domain_of:
    - ProcedureStep
    range: integer
  target_range:
    name: target_range
    description: Target interval for a `minmax_rescale` step (e.g. lo -1, hi 1).
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: ProcedureStep
    domain_of:
    - ProcedureStep
    range: Range
    inlined: true
  name:
    name: name
    description: Globally unique identifier for the entity.
    from_schema: https://w3id.org/tvbo/common
    slot_uri: schema:name
    identifier: true
    owner: ProcedureStep
    domain_of:
    - BrainAtlas
    - CommonCoordinateSpace
    - ParcellationEntity
    - StudyLayout
    - StudyTemplate
    - StudyDirectory
    - StudyFile
    - DBSProtocol
    - ClinicalScale
    - ClinicalScore
    - SoftwarePackage
    - SoftwareRequirement
    - SoftwareEnvironment
    - Figure
    - Event
    - Tractogram
    - ResultEntity
    - Activity
    - CachedArray
    - MeasureSpec
    - NamedArray
    - GraphGenerator
    - Binding
    - ProcedureStep
    - File
    - StateValue
    - Observation
    - Dynamics
    - StateVariable
    - Distribution
    - Parameter
    - CouplingInput
    - Argument
    - Function
    - FunctionCall
    - Callable
    - DerivedParameter
    - DerivedVariable
    - DataSource
    - OptimizationStage
    - Exploration
    - Inference
    - Prior
    - Likelihood
    - UpdateRule
    - Algorithm
    - Option
    - BranchSwitch
    - Continuation
    - Coupling
    - EnvironmentVariable
    - SchedulerDirective
    - Reducer
    range: string
    required: true
  description:
    name: description
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: dcterms:description
    owner: ProcedureStep
    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
class_uri: tvbo:ProcedureStep