Class: Mesh

Triangle (or higher-order) mesh geometry. May stand alone (via mesh_file pointing at an external GIFTI/VTK/MSH file) OR be inlined on a Network as Network.mesh. In the inlined-on-Network case, the vertices are the parent Network’s nodes/coordinates (so coordinates here may be left empty), the faces live in the same h5 companion under a path given by elements (default mesh/faces), and optional per-vertex normals / curvature live alongside. The optional parcel_map_field points at the parent Network’s per-vertex parcel-id array (default nodes/parent_index from the hierarchical-Network pattern, see Network.qmd §7.1).

URI: tvbo:Mesh

 classDiagram
    class Mesh
    click Mesh href "./Mesh.html"
      Mesh : coordinate_space
        
          
    
        
        
        Mesh --> "0..1" CommonCoordinateSpace : coordinate_space
        click CommonCoordinateSpace href "./CommonCoordinateSpace.html"
    

        
      Mesh : coordinates
        
          
    
        
        
        Mesh --> "*" Coordinate : coordinates
        click Coordinate href "./Coordinate.html"
    

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

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

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

        
      Mesh : element_type
        
          
    
        
        
        Mesh --> "0..1" ElementType : element_type
        click ElementType href "../../enums/ElementType.html"
    

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

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

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

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

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

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

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

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

        
      Mesh : parcellation
        
          
    
        
        
        Mesh --> "0..1" Parcellation : parcellation
        click Parcellation href "./Parcellation.html"
    

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

Class Properties

Property Value
Class URI tvbo:Mesh

Slots

Name Cardinality and Range Description Inheritance
label 0..1
xsd:string		 direct
description 0..1
xsd:string		 direct
dataLocation 0..1
xsd:string		 Add the location of the data file containing the parcellation terminology direct
element_type 0..1
ElementType		 direct
coordinates *
Coordinate		 Node coordinates (x,y,z) in the given coordinate space direct
elements 0..1
xsd:string		 Topology indices: either a file reference, or (when inlined on a Network) a d… direct
coordinate_space 0..1
CommonCoordinateSpace		 direct
mesh_file 0..1
xsd:string		 Path to external mesh file (GIFTI, VTK, MSH, FreeSurfer, etc direct
mesh_format 0..1
xsd:string		 Explicit format override (gifti, freesurfer, meshio, vtk, gmsh) direct
number_of_vertices 0..1
xsd:integer		 Number of vertices in the mesh direct
number_of_elements 0..1
xsd:integer		 Number of elements (triangles, quads, tetrahedra, etc direct
parcellation 0..1
Parcellation		 Brain parcellation this mesh’s parcel_map indexes into direct
normals 0..1
xsd:string		 Optional path inside the parent Network’s h5 (or an external file) to per-ver… direct
curvature 0..1
xsd:string		 Optional path to per-vertex curvature (N,) float direct
vertices_field 0..1
xsd:string		 When the mesh is inlined on a Network, the dotted path inside the parent’s h5… direct
parcel_map_field 0..1
xsd:string		 When the mesh is inlined on a Network with a parcellation, the dotted path in… direct

Usages

used by used in type used
Network mesh range Mesh
SpatialField mesh range Mesh
FieldStateVariable mesh range Mesh
PDE mesh range Mesh

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Mesh
description: Triangle (or higher-order) mesh geometry. May stand alone (via ``mesh_file``
  pointing at an external GIFTI/VTK/MSH file) OR be inlined on a Network as ``Network.mesh``.
  In the inlined-on-Network case, the vertices are the parent Network's ``nodes/coordinates``
  (so ``coordinates`` here may be left empty), the faces live in the same h5 companion
  under a path given by ``elements`` (default ``mesh/faces``), and optional per-vertex
  ``normals`` / ``curvature`` live alongside. The optional ``parcel_map_field`` points
  at the parent Network's per-vertex parcel-id array (default ``nodes/parent_index``
  from the hierarchical-Network pattern, see Network.qmd §7.1).
from_schema: https://w3id.org/tvbo
slots:
- label
- description
- dataLocation
attributes:
  element_type:
    name: element_type
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Mesh
    range: ElementType
  coordinates:
    name: coordinates
    description: Node coordinates (x,y,z) in the given coordinate space.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Mesh
    range: Coordinate
    multivalued: true
  elements:
    name: elements
    description: 'Topology indices: either a file reference, or (when inlined on a
      Network) a dotted path inside the parent Network''s h5 companion to the (M,
      3) int triangle face array. Default convention: ``mesh/faces``.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Mesh
    range: string
  coordinate_space:
    name: coordinate_space
    from_schema: https://w3id.org/tvbo
    domain_of:
    - DBSDataset
    - DBSSubject
    - Electrode
    - EField
    - Network
    - SpatialDomain
    - Mesh
    range: CommonCoordinateSpace
  mesh_file:
    name: mesh_file
    description: Path to external mesh file (GIFTI, VTK, MSH, FreeSurfer, etc.).
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Mesh
    range: string
  mesh_format:
    name: mesh_format
    description: Explicit format override (gifti, freesurfer, meshio, vtk, gmsh).
      Auto-detected from extension if null.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Mesh
    range: string
  number_of_vertices:
    name: number_of_vertices
    description: Number of vertices in the mesh.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Mesh
    range: integer
  number_of_elements:
    name: number_of_elements
    description: Number of elements (triangles, quads, tetrahedra, etc.).
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Mesh
    range: integer
  parcellation:
    name: parcellation
    description: Brain parcellation this mesh's parcel_map indexes into. Inlined to
      match Network.parcellation's existing pattern. When the mesh is inlined on a
      Network that already declares ``parcellation``, this slot is optional and defaults
      to the parent's value.
    from_schema: https://w3id.org/tvbo
    domain_of:
    - Network
    - Mesh
    range: Parcellation
    inlined: true
  normals:
    name: normals
    description: 'Optional path inside the parent Network''s h5 (or an external file)
      to per-vertex normals (N, 3) float. Default convention: ``mesh/normals``.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Mesh
    range: string
  curvature:
    name: curvature
    description: 'Optional path to per-vertex curvature (N,) float. Default convention:
      ``mesh/curvature``.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Mesh
    range: string
  vertices_field:
    name: vertices_field
    description: 'When the mesh is inlined on a Network, the dotted path inside the
      parent''s h5 to vertex coordinates. Default: ``nodes/coordinates``.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Mesh
    range: string
  parcel_map_field:
    name: parcel_map_field
    description: 'When the mesh is inlined on a Network with a parcellation, the dotted
      path inside the parent''s h5 to the per-vertex parcel id array. Default: ``nodes/parent_index``.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Mesh
    range: string
class_uri: tvbo:Mesh

Induced

name: Mesh
description: Triangle (or higher-order) mesh geometry. May stand alone (via ``mesh_file``
  pointing at an external GIFTI/VTK/MSH file) OR be inlined on a Network as ``Network.mesh``.
  In the inlined-on-Network case, the vertices are the parent Network's ``nodes/coordinates``
  (so ``coordinates`` here may be left empty), the faces live in the same h5 companion
  under a path given by ``elements`` (default ``mesh/faces``), and optional per-vertex
  ``normals`` / ``curvature`` live alongside. The optional ``parcel_map_field`` points
  at the parent Network's per-vertex parcel-id array (default ``nodes/parent_index``
  from the hierarchical-Network pattern, see Network.qmd §7.1).
from_schema: https://w3id.org/tvbo
attributes:
  element_type:
    name: element_type
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Mesh
    domain_of:
    - Mesh
    range: ElementType
  coordinates:
    name: coordinates
    description: Node coordinates (x,y,z) in the given coordinate space.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Mesh
    domain_of:
    - Mesh
    range: Coordinate
    multivalued: true
  elements:
    name: elements
    description: 'Topology indices: either a file reference, or (when inlined on a
      Network) a dotted path inside the parent Network''s h5 companion to the (M,
      3) int triangle face array. Default convention: ``mesh/faces``.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Mesh
    domain_of:
    - Mesh
    range: string
  coordinate_space:
    name: coordinate_space
    from_schema: https://w3id.org/tvbo
    owner: Mesh
    domain_of:
    - DBSDataset
    - DBSSubject
    - Electrode
    - EField
    - Network
    - SpatialDomain
    - Mesh
    range: CommonCoordinateSpace
  mesh_file:
    name: mesh_file
    description: Path to external mesh file (GIFTI, VTK, MSH, FreeSurfer, etc.).
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Mesh
    domain_of:
    - Mesh
    range: string
  mesh_format:
    name: mesh_format
    description: Explicit format override (gifti, freesurfer, meshio, vtk, gmsh).
      Auto-detected from extension if null.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Mesh
    domain_of:
    - Mesh
    range: string
  number_of_vertices:
    name: number_of_vertices
    description: Number of vertices in the mesh.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Mesh
    domain_of:
    - Mesh
    range: integer
  number_of_elements:
    name: number_of_elements
    description: Number of elements (triangles, quads, tetrahedra, etc.).
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Mesh
    domain_of:
    - Mesh
    range: integer
  parcellation:
    name: parcellation
    description: Brain parcellation this mesh's parcel_map indexes into. Inlined to
      match Network.parcellation's existing pattern. When the mesh is inlined on a
      Network that already declares ``parcellation``, this slot is optional and defaults
      to the parent's value.
    from_schema: https://w3id.org/tvbo
    owner: Mesh
    domain_of:
    - Network
    - Mesh
    range: Parcellation
    inlined: true
  normals:
    name: normals
    description: 'Optional path inside the parent Network''s h5 (or an external file)
      to per-vertex normals (N, 3) float. Default convention: ``mesh/normals``.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Mesh
    domain_of:
    - Mesh
    range: string
  curvature:
    name: curvature
    description: 'Optional path to per-vertex curvature (N,) float. Default convention:
      ``mesh/curvature``.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Mesh
    domain_of:
    - Mesh
    range: string
  vertices_field:
    name: vertices_field
    description: 'When the mesh is inlined on a Network, the dotted path inside the
      parent''s h5 to vertex coordinates. Default: ``nodes/coordinates``.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Mesh
    domain_of:
    - Mesh
    range: string
  parcel_map_field:
    name: parcel_map_field
    description: 'When the mesh is inlined on a Network with a parcellation, the dotted
      path inside the parent''s h5 to the per-vertex parcel id array. Default: ``nodes/parent_index``.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Mesh
    domain_of:
    - Mesh
    range: string
  label:
    name: label
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: rdfs:label
    owner: Mesh
    domain_of:
    - ParcellationTerminology
    - Subject
    - Session
    - Dataset
    - Contact
    - SoftwareEnvironment
    - Equation
    - Stimulus
    - Event
    - Parcellation
    - Tractogram
    - Matrix
    - Phenotype
    - Network
    - Node
    - Edge
    - Observation
    - Dynamics
    - StateVariable
    - Parameter
    - Function
    - FunctionCall
    - DerivedVariable
    - RandomStream
    - DataSource
    - OptimizationStage
    - Exploration
    - ExplorationAxis
    - FreeParameter
    - Inference
    - AlgorithmStage
    - TuningObjective
    - Continuation
    - Coupling
    - RegionMapping
    - SimulationExperiment
    - SimulationStudy
    - TimeSeries
    - NDArray
    - SpatialDomain
    - Mesh
    - SpatialField
    - FieldStateVariable
    - DifferentialOperator
    - BoundaryCondition
    - PDESolver
    - PDE
    range: string
  description:
    name: description
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: dcterms:description
    owner: Mesh
    domain_of:
    - Dataset
    - ClinicalScore
    - SoftwarePackage
    - SoftwareRequirement
    - SoftwareEnvironment
    - Equation
    - Stimulus
    - Event
    - Tractogram
    - Matrix
    - 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
    - TimeSeries
    - NDArray
    - SpatialDomain
    - Mesh
    - SpatialField
    - FieldStateVariable
    - BoundaryCondition
    - PDESolver
    - PDE
    range: string
  dataLocation:
    name: dataLocation
    description: Add the location of the data file containing the parcellation terminology.
    from_schema: https://openminds.ebrains.eu/sands/BrainAtlas
    owner: Mesh
    domain_of:
    - ParcellationTerminology
    - SoftwareRequirement
    - SoftwareEnvironment
    - Stimulus
    - Event
    - Matrix
    - Dynamics
    - RandomStream
    - RegionMapping
    - TimeSeries
    - NDArray
    - Mesh
    range: string
class_uri: tvbo:Mesh