SpatialDataArray

The SpatialDataImage and -Label classes represent elements from a SpatialData's images/ and labels/ layers, respectively. In both cases, these are represented as a ZarrArray (data slot), and associated with .zattrs represented as SpatialDataAttrs (meta slot); a list of metadata stores other arbitrary info.

Currently defined methods (here, x is a SpatialDataArray):

• data/meta(x) access underlying data/.zattrs

• data_type(x) gets the underlying data type (e.g., float64)

• channels(x) gets channel names (applies to images only)

• dim(x) returns the dimensions of data(x)

• length(x) returns the length of data(x)

Usage

SpatialDataImage(
  data = list(),
  meta = SpatialDataAttrs(),
  metadata = list(),
  ...
)

SpatialDataLabel(
  data = list(),
  meta = SpatialDataAttrs(),
  metadata = list(),
  ...
)

# S4 method for class 'SpatialDataArray'
dim(x)

# S4 method for class 'SpatialDataArray'
length(x)

# S4 method for class 'SpatialDataArray'
data_type(x)

# S4 method for class 'DelayedArray'
data_type(x)

# S4 method for class 'SpatialDataAttrs'
channels(x, ...)

# S4 method for class 'SpatialDataImage'
channels(x, ...)

# S4 method for class 'SpatialDataElement'
channels(x, ...)

# S4 method for class 'SpatialDataImage,ANY,ANY,ANY'
x[i, j, k, ..., drop = FALSE]

# S4 method for class 'SpatialDataLabel,ANY,ANY,ANY'
x[i, j, ..., drop = FALSE]

Arguments

data

list of ZarrArrays

meta

SpatialDataAttrs

metadata

optional list of arbitrary additional content.

...

option arguments passed to and from other methods.

x

SpatialDataArray

i, j, k

indices specifying elements/slices to extract.

drop

ignored.

Value

SpatialDataArray

Examples

zs <- file.path("extdata", "blobs.zarr")
zs <- system.file(zs, package="SpatialData")

# get path to 'i'th element in layer 'l'
fn <- \(l, i=1) list.dirs(file.path(zs, l), recursive=FALSE)[i]

# label
(x <- readLabel(fn("labels")))
#> class:  SpatialDataLabel  
#> Scales (1): (64,64)
x[1:10, 1:10]
#> class:  SpatialDataLabel  
#> Scales (1): (10,10)
meta(x)
#> class: SpatialDataAttrs
#> axes(2):
#> - name: y x 
#> - type: space space 
#> coordTrans(5):
#> - global: (identity)
#> - scale: (scale:[3,2])
#> - translation: (translation:[-50,10])
#> - affine: (affine:[[20,10,30],[50,40,60]])
#> - sequence: (scale:[3,2]), (translation:[-50,10])
#> datasets(1): 0
#> - 0: (scale:[1,1])

# image
readImage(fn("images"))
#> class:  SpatialDataImage  
#> Scales (1): (3,64,64)

# multi-scale
(x <- readImage(fn("images", 2)))
#> class:  SpatialDataImage (MultiScale) 
#> Scales (3): (3,64,64 3,32,32 3,16,16)

channels(x)
#> label label label 
#>     0     1     2 
dim(data(x, 1))   # highest res.
#> [1]  3 64 64
dim(data(x, Inf)) # lowest res.
#> [1]  3 16 16

# RGB visual
rgb <- apply(
  data(x, 1), c(2, 3), 
  \(.) rgb(.[1], .[2], .[3]))
plot(
  row(rgb), col(rgb), col=rgb, 
  pch=15, asp=1, ylim=c(ncol(rgb), 0))