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Coord. trans. utilities

Source: R/CTutils.R
CTutils.Rd

Coord. trans. utilities

Usage

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

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

# S4 method for class 'SpatialDataAttrs'
CTdata(x, i = 1, ...)

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

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

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

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

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

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

# S4 method for class 'SpatialDataElement'
CTdata(x, i = 1, ...)

# S4 method for class 'SpatialData'
CTname(x, ...)

# S4 method for class 'SpatialDataElement'
rmvCT(x, i)

# S4 method for class 'SpatialDataAttrs'
rmvCT(x, i)

# S4 method for class 'SpatialDataElement'
addCT(x, name, type = "identity", data = NULL)

# S4 method for class 'SpatialDataAttrs'
addCT(x, name, type = "identity", data = NULL)

Arguments

x

SpatialData, an element, or SpatialDataAttrs.

...

option arguments passed to and from other methods.

i

for CTpath, source node label; else, string or scalar integer giving the name or index of a coordinate space.

name

character(1); name of coordinate space

type

character(1); type of transformation

data

transformation data; size and shape depend on transformation and element type (e.g., numeric(1) for rotation, numeric(2) for scaling in 2D)

Value

  • CTname: character string; transformation name (e.g., "global")

  • CTtype: character string; transformation type (e.g., "affine")

  • CTdata: list; transformation data (e.g., scalar numeric for rotation)

  • CTlist: list; list of transformation specifications per OME-NGFF spec

  • add/rmvCT: SpatialDataElement or SpatialDataAttrs with transformation(s) added/removed

  • axes: list; each element is a character string (name), or list with axis name and type (e.g., "space" or "channel")

Examples

x <- file.path("extdata", "blobs.zarr")
x <- system.file(x, package="SpatialData")
x <- readSpatialData(x, tables=FALSE)

# view available target coordinate systems
CTname(z <- meta(label(x)))
#> [1] "global"      "scale"       "translation" "affine"      "sequence"   

# add
addCT(z, "scale", "scale", c(12, 34)) # overwrite
#> class: SpatialDataAttrs
#> axes(2):
#> - name: y x 
#> - type: space space 
#> coordTrans(5):
#> - global: (identity)
#> - scale: (scale:[12,34])
#> - 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])
CTname(addCT(z, "new", "translation", c(12, 34)))
#> [1] "global"      "scale"       "translation" "affine"      "sequence"   
#> [6] "new"        

# rmv
CTname(rmvCT(z, 2))        # by index
#> [1] "global"      "translation" "affine"      "sequence"   
CTname(rmvCT(z, "scale"))  # by name
#> [1] "global"      "translation" "affine"      "sequence"   
CTname(rmvCT(z, "global")) # identity is protected
#> Warning: can't drop identity
#> [1] "global"      "scale"       "translation" "affine"      "sequence"