Class: Volume

A labelled-volume panel’s geometry: the volumetric counterpart of Surface, same layer and same colour scale, with the geometry coming from an atlas instead of a mesh. Values are placed BY LABEL through the atlas crosswalk, never by array position.

URI: tvbo:class/Volume

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

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

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

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

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

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

        
      Volume : view
        
          
    
        
        
        Volume --> "0..1" VolumeView : view
        click VolumeView href "../../enums/VolumeView.html"
    

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

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

Inheritance

ColorScale
- Volume

Slots

Name	Cardinality and Range	Description	Inheritance
atlas	0..1 xsd:string	The curated atlas whose segmentation the values are painted into	direct
image	0..1 xsd:string	A `dseg` segmentation file, for a parcellation nobody has curated	direct
view	0..1 VolumeView	Which plane the volume is projected along	direct
intensity_projection	0..1 xsd:string	How voxels collapse along the view axis (`absmax` by default)	direct
colormap	0..1 xsd:string	The scale, as a key of the theme’s `colormaps` (`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	volume	range	Volume
Inset	volume	range	Volume

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Volume
description: 'A labelled-volume panel''s geometry: the volumetric counterpart of `Surface`,
  same layer and same colour scale, with the geometry coming from an atlas instead
  of a mesh. Values are placed BY LABEL through the atlas crosswalk, never by array
  position.'
from_schema: https://w3id.org/tvbo/figure
is_a: ColorScale
attributes:
  atlas:
    name: atlas
    description: The curated atlas whose segmentation the values are painted into.
    from_schema: https://w3id.org/tvbo/figure
    domain_of:
    - Surface
    - Volume
    - Parcellation
    - BidsEntities
    range: string
  image:
    name: image
    description: A `dseg` segmentation file, for a parcellation nobody has curated.
    from_schema: https://w3id.org/tvbo/figure
    rank: 1000
    domain_of:
    - Volume
    range: string
  view:
    name: view
    description: Which plane the volume is projected along.
    from_schema: https://w3id.org/tvbo/figure
    domain_of:
    - Surface
    - Volume
    range: VolumeView
  intensity_projection:
    name: intensity_projection
    description: How voxels collapse along the view axis (`absmax` by default).
    from_schema: https://w3id.org/tvbo/figure
    rank: 1000
    domain_of:
    - Volume
    range: string

Induced

name: Volume
description: 'A labelled-volume panel''s geometry: the volumetric counterpart of `Surface`,
  same layer and same colour scale, with the geometry coming from an atlas instead
  of a mesh. Values are placed BY LABEL through the atlas crosswalk, never by array
  position.'
from_schema: https://w3id.org/tvbo/figure
is_a: ColorScale
attributes:
  atlas:
    name: atlas
    description: The curated atlas whose segmentation the values are painted into.
    from_schema: https://w3id.org/tvbo/figure
    owner: Volume
    domain_of:
    - Surface
    - Volume
    - Parcellation
    - BidsEntities
    range: string
  image:
    name: image
    description: A `dseg` segmentation file, for a parcellation nobody has curated.
    from_schema: https://w3id.org/tvbo/figure
    rank: 1000
    owner: Volume
    domain_of:
    - Volume
    range: string
  view:
    name: view
    description: Which plane the volume is projected along.
    from_schema: https://w3id.org/tvbo/figure
    owner: Volume
    domain_of:
    - Surface
    - Volume
    range: VolumeView
  intensity_projection:
    name: intensity_projection
    description: How voxels collapse along the view axis (`absmax` by default).
    from_schema: https://w3id.org/tvbo/figure
    rank: 1000
    owner: Volume
    domain_of:
    - Volume
    range: string
  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: Volume
    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: Volume
    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: Volume
    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: Volume
    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: Volume
    domain_of:
    - ColorScale
    range: float