Class: Surface

A cortical surface panel’s geometry and how a field is painted on it. One object, so the three mutually exclusive places a mesh can come from — a tvbo Network carrying one, a mesh file, or a named template — sit together with the options that only apply to each, instead of being loose names that could be given in any combination.

URI: tvbo:class/Surface

 classDiagram
    class Surface
    click Surface href "./Surface.html"
      ColorScale <|-- Surface
        click ColorScale href "./ColorScale.html"
      
      Surface : atlas
        
          
    
        
        
        Surface --> "0..1" String : atlas
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

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

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

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

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

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

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

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

        
      Surface : hemi
        
          
    
        
        
        Surface --> "0..1" Hemisphere : hemi
        click Hemisphere href "../../enums/Hemisphere.html"
    

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

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

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

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

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

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

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

        
      Surface : view
        
          
    
        
        
        Surface --> "0..1" SurfaceView : view
        click SurfaceView href "../../enums/SurfaceView.html"
    

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

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

Inheritance

Slots

Name Cardinality and Range Description Inheritance
connectome 0..1
xsd:string		 A tvbo Network whose companion carries a mesh group direct
mesh 0..1
xsd:string		 A surface mesh file — GIFTI, VTK, FreeSurfer, or an | direct | | [mesh_format](../slots/mesh_format.qmd) | 0..1 <br/> [xsd:string](http://www.w3.org/2001/XMLSchema#string) | The mesh file's format, where the extension does not say | direct | | [template](../slots/template.qmd) | 0..1 <br/> [xsd:string](http://www.w3.org/2001/XMLSchema#string) | A named template surface (fsaverage), fetched rather than committed, so a p... | direct | | [density](../slots/density.qmd) | 0..1 <br/> [xsd:string](http://www.w3.org/2001/XMLSchema#string) | The template's vertex density (164k) | direct | | [hemi](../slots/hemi.qmd) | 0..1 <br/> [Hemisphere](../enums/Hemisphere.qmd) | Which hemisphere to draw (left,right, orbothjoined into one mesh — w... | direct | | [view](../slots/view.qmd) | 0..1 <br/> [SurfaceView](../enums/SurfaceView.qmd) | Where the camera sits | direct | | [atlas](../slots/atlas.qmd) | 0..1 <br/> [xsd:string](http://www.w3.org/2001/XMLSchema#string) | The parcellation the layer's per-region values are placed through, BY LABEL —... | direct | | [surface_atlas](../slots/surface_atlas.qmd) | 0..1 <br/> [xsd:string](http://www.w3.org/2001/XMLSchema#string) | The atlas to read vertex labels from, where it differs from the one the value... | direct | | [mask](../slots/mask.qmd) | 0..1 <br/> [xsd:string](http://www.w3.org/2001/XMLSchema#string) | A per-vertex 0/1 file | direct | | [geometry](../slots/geometry.qmd) | 0..1 <br/> [xsd:boolean](http://www.w3.org/2001/XMLSchema#boolean) | Read the layer as (V, 3) vertex COORDINATES rather than as a field: what the ... | direct | | [color](../slots/color.qmd) | 0..1 <br/> [xsd:string](http://www.w3.org/2001/XMLSchema#string) | Draw the mesh itself in one flat colour instead of painting a map on it | direct | | [edge_color](../slots/edge_color.qmd) | 0..1 <br/> [xsd:string](http://www.w3.org/2001/XMLSchema#string) | Draw the triangulation in this colour, for a panel whose subject is the mesh ... | direct | | [edge_width](../slots/edge_width.qmd) | 0..1 <br/> [xsd:float](http://www.w3.org/2001/XMLSchema#float) | Line weight of the triangulation | direct | | [colormap](../slots/colormap.qmd) | 0..1 <br/> [xsd:string](http://www.w3.org/2001/XMLSchema#string) | The scale, as a key of the theme'scolormaps(sequential,diverging`, or… ColorScale
vmin 0..1
xsd:float		 The value the scale starts at ColorScale
vmax 0..1
xsd:float		 The value the scale ends at ColorScale
symmetric 0..1
xsd:boolean		 Centre the limits on zero, so zero is the map’s midpoint ColorScale
percentile 0..1
xsd:float		 Clip the limit to this percentile of the values (100 = no clipping), so one o… ColorScale

Usages

used by used in type used
Panel surface range Surface
Inset surface range Surface

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Surface
description: A cortical surface panel's geometry and how a field is painted on it.
  One object, so the three mutually exclusive places a mesh can come from — a tvbo
  `Network` carrying one, a mesh file, or a named template — sit together with the
  options that only apply to each, instead of being loose names that could be given
  in any combination.
from_schema: https://w3id.org/tvbo/figure
is_a: ColorScale
attributes:
  connectome:
    name: connectome
    description: A tvbo `Network` whose companion carries a mesh group. Geometry belongs
      to the network, so a study that has one needs no mesh file beside it.
    from_schema: https://w3id.org/tvbo/figure
    rank: 1000
    domain_of:
    - Surface
    - Graph
    range: string
  mesh:
    name: mesh
    description: A surface mesh file — GIFTI, VTK, FreeSurfer, or an `.npz` holding
      `vertices`/`faces` for a mesh an analysis derived rather than measured.
    from_schema: https://w3id.org/tvbo/figure
    rank: 1000
    domain_of:
    - Surface
    - Network
    - SpatialField
    - FieldStateVariable
    - PDE
    range: string
  mesh_format:
    name: mesh_format
    description: The mesh file's format, where the extension does not say.
    from_schema: https://w3id.org/tvbo/figure
    rank: 1000
    domain_of:
    - Surface
    - Mesh
    range: string
  template:
    name: template
    description: A named template surface (`fsaverage`), fetched rather than committed,
      so a parcellated map needs no mesh checked in beside the page.
    from_schema: https://w3id.org/tvbo/figure
    domain_of:
    - StudyFile
    - LayoutTemplateVariant
    - Surface
    - BidsEntities
    range: string
  density:
    name: density
    description: The template's vertex density (`164k`). Applies only to `template`.
    from_schema: https://w3id.org/tvbo/figure
    rank: 1000
    domain_of:
    - Surface
    range: string
  hemi:
    name: hemi
    description: Which hemisphere to draw (`left`, `right`, or `both` joined into
      one mesh — what a paper prints for a dorsal view). Applies only to `template`.
      The vocabulary is the schema's own, shared with everything else that names a
      hemisphere.
    from_schema: https://w3id.org/tvbo/figure
    rank: 1000
    domain_of:
    - Surface
    - BidsEntities
    range: Hemisphere
  view:
    name: view
    description: Where the camera sits.
    from_schema: https://w3id.org/tvbo/figure
    rank: 1000
    domain_of:
    - Surface
    - Volume
    range: SurfaceView
  atlas:
    name: atlas
    description: The parcellation the layer's per-region values are placed through,
      BY LABEL — a per-region array ordered differently would otherwise paint every
      region with its neighbour's number and still look like a brain.
    from_schema: https://w3id.org/tvbo/figure
    rank: 1000
    domain_of:
    - Surface
    - Volume
    - Parcellation
    - BidsEntities
    range: string
  surface_atlas:
    name: surface_atlas
    description: The atlas to read vertex labels from, where it differs from the one
      the values are keyed by.
    from_schema: https://w3id.org/tvbo/figure
    rank: 1000
    domain_of:
    - Surface
    range: string
  mask:
    name: mask
    description: A per-vertex 0/1 file. Vertices OUTSIDE it — a medial wall — are
      drawn grey and kept out of the colour range rather than coloured as zeros.
    from_schema: https://w3id.org/tvbo/figure
    rank: 1000
    domain_of:
    - Surface
    range: string
  geometry:
    name: geometry
    description: 'Read the layer as (V, 3) vertex COORDINATES rather than as a field:
      what the panel then shows is the surface a reconstruction rebuilt, not a quantity
      living on a fixed one.'
    from_schema: https://w3id.org/tvbo/figure
    rank: 1000
    domain_of:
    - Surface
    - SpatialDomain
    range: boolean
  color:
    name: color
    description: Draw the mesh itself in one flat colour instead of painting a map
      on it. With no layer, that is the bare geometry.
    from_schema: https://w3id.org/tvbo/figure
    domain_of:
    - ParcellationEntity
    - Encoding
    - Annotation
    - Style
    - Surface
    - Graph
    - Rule
    - Region
    range: string
  edge_color:
    name: edge_color
    description: Draw the triangulation in this colour, for a panel whose subject
      is the mesh the model is solved on.
    from_schema: https://w3id.org/tvbo/figure
    rank: 1000
    domain_of:
    - Surface
    - Graph
    range: string
  edge_width:
    name: edge_width
    description: Line weight of the triangulation.
    from_schema: https://w3id.org/tvbo/figure
    rank: 1000
    domain_of:
    - Surface
    - Graph
    range: float

Induced

name: Surface
description: A cortical surface panel's geometry and how a field is painted on it.
  One object, so the three mutually exclusive places a mesh can come from — a tvbo
  `Network` carrying one, a mesh file, or a named template — sit together with the
  options that only apply to each, instead of being loose names that could be given
  in any combination.
from_schema: https://w3id.org/tvbo/figure
is_a: ColorScale
attributes:
  connectome:
    name: connectome
    description: A tvbo `Network` whose companion carries a mesh group. Geometry belongs
      to the network, so a study that has one needs no mesh file beside it.
    from_schema: https://w3id.org/tvbo/figure
    rank: 1000
    owner: Surface
    domain_of:
    - Surface
    - Graph
    range: string
  mesh:
    name: mesh
    description: A surface mesh file — GIFTI, VTK, FreeSurfer, or an `.npz` holding
      `vertices`/`faces` for a mesh an analysis derived rather than measured.
    from_schema: https://w3id.org/tvbo/figure
    rank: 1000
    owner: Surface
    domain_of:
    - Surface
    - Network
    - SpatialField
    - FieldStateVariable
    - PDE
    range: string
  mesh_format:
    name: mesh_format
    description: The mesh file's format, where the extension does not say.
    from_schema: https://w3id.org/tvbo/figure
    rank: 1000
    owner: Surface
    domain_of:
    - Surface
    - Mesh
    range: string
  template:
    name: template
    description: A named template surface (`fsaverage`), fetched rather than committed,
      so a parcellated map needs no mesh checked in beside the page.
    from_schema: https://w3id.org/tvbo/figure
    owner: Surface
    domain_of:
    - StudyFile
    - LayoutTemplateVariant
    - Surface
    - BidsEntities
    range: string
  density:
    name: density
    description: The template's vertex density (`164k`). Applies only to `template`.
    from_schema: https://w3id.org/tvbo/figure
    rank: 1000
    owner: Surface
    domain_of:
    - Surface
    range: string
  hemi:
    name: hemi
    description: Which hemisphere to draw (`left`, `right`, or `both` joined into
      one mesh — what a paper prints for a dorsal view). Applies only to `template`.
      The vocabulary is the schema's own, shared with everything else that names a
      hemisphere.
    from_schema: https://w3id.org/tvbo/figure
    rank: 1000
    owner: Surface
    domain_of:
    - Surface
    - BidsEntities
    range: Hemisphere
  view:
    name: view
    description: Where the camera sits.
    from_schema: https://w3id.org/tvbo/figure
    rank: 1000
    owner: Surface
    domain_of:
    - Surface
    - Volume
    range: SurfaceView
  atlas:
    name: atlas
    description: The parcellation the layer's per-region values are placed through,
      BY LABEL — a per-region array ordered differently would otherwise paint every
      region with its neighbour's number and still look like a brain.
    from_schema: https://w3id.org/tvbo/figure
    rank: 1000
    owner: Surface
    domain_of:
    - Surface
    - Volume
    - Parcellation
    - BidsEntities
    range: string
  surface_atlas:
    name: surface_atlas
    description: The atlas to read vertex labels from, where it differs from the one
      the values are keyed by.
    from_schema: https://w3id.org/tvbo/figure
    rank: 1000
    owner: Surface
    domain_of:
    - Surface
    range: string
  mask:
    name: mask
    description: A per-vertex 0/1 file. Vertices OUTSIDE it — a medial wall — are
      drawn grey and kept out of the colour range rather than coloured as zeros.
    from_schema: https://w3id.org/tvbo/figure
    rank: 1000
    owner: Surface
    domain_of:
    - Surface
    range: string
  geometry:
    name: geometry
    description: 'Read the layer as (V, 3) vertex COORDINATES rather than as a field:
      what the panel then shows is the surface a reconstruction rebuilt, not a quantity
      living on a fixed one.'
    from_schema: https://w3id.org/tvbo/figure
    rank: 1000
    owner: Surface
    domain_of:
    - Surface
    - SpatialDomain
    range: boolean
  color:
    name: color
    description: Draw the mesh itself in one flat colour instead of painting a map
      on it. With no layer, that is the bare geometry.
    from_schema: https://w3id.org/tvbo/figure
    owner: Surface
    domain_of:
    - ParcellationEntity
    - Encoding
    - Annotation
    - Style
    - Surface
    - Graph
    - Rule
    - Region
    range: string
  edge_color:
    name: edge_color
    description: Draw the triangulation in this colour, for a panel whose subject
      is the mesh the model is solved on.
    from_schema: https://w3id.org/tvbo/figure
    rank: 1000
    owner: Surface
    domain_of:
    - Surface
    - Graph
    range: string
  edge_width:
    name: edge_width
    description: Line weight of the triangulation.
    from_schema: https://w3id.org/tvbo/figure
    rank: 1000
    owner: Surface
    domain_of:
    - Surface
    - Graph
    range: float
  colormap:
    name: colormap
    description: The scale, as a key of the theme's `colormaps` (`sequential`, `diverging`,
      or one a project added) or a name the backend knows. Unset takes the theme's
      `sequential`, or its `diverging` where the scale is centred.
    from_schema: https://w3id.org/tvbo/figure
    owner: Surface
    domain_of:
    - Style
    - ColorScale
    range: string
  vmin:
    name: vmin
    description: The value the scale starts at. A declared end is honoured as given;
      the other is still derived from the data.
    from_schema: https://w3id.org/tvbo/figure
    rank: 1000
    owner: Surface
    domain_of:
    - ColorScale
    range: float
  vmax:
    name: vmax
    description: The value the scale ends at. See `vmin`.
    from_schema: https://w3id.org/tvbo/figure
    rank: 1000
    owner: Surface
    domain_of:
    - ColorScale
    range: float
  symmetric:
    name: symmetric
    description: Centre the limits on zero, so zero is the map's midpoint. What a
      field of signed deviations needs — read on an off-centre scale it is misleading
      in a way no axis label catches.
    from_schema: https://w3id.org/tvbo/figure
    rank: 1000
    owner: Surface
    domain_of:
    - ColorScale
    range: boolean
  percentile:
    name: percentile
    description: Clip the limit to this percentile of the values (100 = no clipping),
      so one outlier region cannot wash the whole map out. Applies whether or not
      the scale is centred.
    from_schema: https://w3id.org/tvbo/figure
    rank: 1000
    owner: Surface
    domain_of:
    - ColorScale
    range: float