spatialdataR/man/SpatialDataArray.Rd at d22ce2e915e5d06c44a8564fe565ce391fb28a8e · HelenaLC/spatialdataR · GitHub

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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/sdArray.R
\name{SpatialDataArray}
\alias{SpatialDataArray}
\alias{data_type}
\alias{channels}
\alias{SpatialDataImage}
\alias{SpatialDataLabel}
\alias{dim,SpatialDataArray-method}
\alias{length,SpatialDataArray-method}
\alias{data_type,SpatialDataArray-method}
\alias{data_type,DelayedArray-method}
\alias{channels,SpatialDataAttrs-method}
\alias{channels,SpatialDataImage-method}
\alias{channels,SpatialDataElement-method}
\alias{.sub_sda}
\title{\code{SpatialDataArray}}
\usage{
SpatialDataImage(
  data = list(),
  meta = SpatialDataAttrs(),
  metadata = list(),
  ...
)

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

\S4method{dim}{SpatialDataArray}(x)

\S4method{length}{SpatialDataArray}(x)

\S4method{data_type}{SpatialDataArray}(x)

\S4method{data_type}{DelayedArray}(x)

\S4method{channels}{SpatialDataAttrs}(x, ...)

\S4method{channels}{SpatialDataImage}(x, ...)

\S4method{channels}{SpatialDataElement}(x, ...)

.sub_sda(x, yx, z = list())
}
\arguments{
\item{data}{list of \code{ZarrArray}s}

\item{meta}{\code{\link{SpatialDataAttrs}}}

\item{metadata}{optional list of arbitrary additional content.}

\item{...}{option arguments passed to and from other methods.}

\item{x}{\code{SpatialDataArray}}

\item{i, j, k}{indices specifying elements/slices to extract.}

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

Currently defined methods (here, \code{x} is a \code{SpatialDataArray}):
\itemize{
\item \code{data/meta(x)} access underlying data/.zattrs
\item \code{data_type(x)} gets the underlying data type (e.g., float64)
\item \code{channels(x)} gets channel names (applies to images only)
\item \code{dim(x)} returns the dimensions of \code{data(x)}
\item \code{length(x)} returns the length of \code{data(x)}
}
}
\examples{
zs <- file.path("extdata", "blobs.zarr")
zs <- system.file(zs, package="spatialdataR")

# 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")))
x[1:10, 1:10]
meta(x)

# image
readImage(fn("images"))

# multi-scale
(x <- readImage(fn("images", 2)))

channels(x)
dim(data(x, 1))   # highest res.
dim(data(x, Inf)) # lowest res.

# 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))
}