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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/SpatialImage.R
\name{SpatialImage-class}
\alias{SpatialImage-class}
\alias{SpatialImage}
\alias{VirtualSpatialImage-class}
\alias{LoadedSpatialImage-class}
\alias{StoredSpatialImage-class}
\alias{RemoteSpatialImage-class}
\alias{dim,VirtualSpatialImage-method}
\alias{dim,StoredSpatialImage-method}
\alias{imgRaster}
\alias{imgRaster,LoadedSpatialImage-method}
\alias{imgRaster,StoredSpatialImage-method}
\alias{imgRaster,RemoteSpatialImage-method}
\alias{imgRaster<-}
\alias{imgRaster<-,LoadedSpatialImage-method}
\alias{imgSource}
\alias{imgSource,LoadedSpatialImage-method}
\alias{imgSource,StoredSpatialImage-method}
\alias{imgSource,RemoteSpatialImage-method}
\alias{imgSource<-}
\alias{imgSource<-,StoredSpatialImage,character-method}
\alias{imgSource<-,RemoteSpatialImage,character-method}
\alias{coerce,VirtualSpatialImage,LoadedSpatialImage-method}
\alias{coerce,RemoteSpatialImage,StoredSpatialImage-method}
\alias{rotateImg}
\alias{rotateImg,VirtualSpatialImage-method}
\alias{rotateImg,LoadedSpatialImage-method}
\alias{mirrorImg}
\alias{mirrorImg,VirtualSpatialImage-method}
\alias{mirrorImg,LoadedSpatialImage-method}
\title{The \code{SpatialImage} class}
\description{
The \code{SpatialImage} class hierarchy provides representations of images
from a variety of sources. It is used by the \linkS4class{SpatialExperiment}
class to manage the loading of images across multiple studies.
}
\section{Constructor}{
\code{SpatialImage(x, is.url)} will return a \code{SpatialImage} object.
The class of the object depends on the type of \code{x}:
\itemize{
\item If \code{x} is a raster object, a \code{LoadedSpatialImage} is
returned. This represents an image that is fully realized into memory,
where the raster representation is stored inside the output object.
\item If \code{x} is a string and \code{is.url=TRUE} or it starts with
\code{"http://"}, \code{"http://"} or \code{"ftp://"},
a \code{RemoteSpatialImage} is returned. This represents an image
that is remotely hosted and retrieved only on request.
\item If \code{x} is a string and \code{is.url=TRUE} or it does not
start with a URL-like prefix, a \code{StoredSpatialImage} is returned.
This represents an image that is stored in a local file
and is loaded into memory only on request.
}
}
\section{Getting the raster image}{
For a \code{SpatialImage} object \code{x}, \code{imgRaster(x, ...)}
will return a raster object (see \code{?\link{as.raster}}).
This is effectively a matrix of RGB colors for each pixel in the image.
For a \code{StoredSpatialImage} object \code{x}, additional arguments
in \code{...} are passed to \code{\link{image_read}}.
This controls how the image is read into memory.
For a \code{RemoteSpatialImage} object \code{x}, the image file is first
downloaded before the raster is returned. Here, \code{...} may contain an
extra \code{cache} argument, which should be a \code{BiocFileCache} object
(from the \pkg{BiocFileCache} package) specifying the file cache location.
The default location is determined by
\code{options("SpatialExperiment.remote.cache.path")},
otherwise it defaults to a subdirectory in the R temporary directory.
Any further named arguments in \code{...} are passed to \code{image_read}.
\code{as.raster(x, ...)} is the same as \code{imgRaster(x, ...)}.
}
\section{In-memory caching}{
For \code{StoredSpatialImage} and \code{RemoteSpatialImage} objects,
loading the image with \code{imgRaster} will automatically
store the loaded raster object in an in-memory cache.
Any subsequent \code{imgRaster} call will retrieve the raster
from the cache, avoiding costly retrieval from the file system.
The cache policy is to evict the least recently used images when
a new image would be added that exceeds the maximum cache size.
If the new image by itself exceeds the maximum cache size, all images are
evicted from the cache to trigger garbage collection and free up memory.
By default, the maximum size of the cache is 4 GB. This can be
modified by setting \code{options("SpatialExperiment.cache.size")}
to some number of bytes, e.g., \code{2^32}.
}
\section{Transformations}{
Two basic image transformations are currently
supported for any \code{SpatialImage} \code{x}, namely,
\code{rotateImg(x, degrees)} for clockwise (\code{degrees > 0}) and
counter-clockwise (\code{degrees < 0}) rotation, and
\code{mirrorImg(x, axis)} for horizontal (\code{axis = "h"}) and
vertical (\code{axis = "v"}) mirroring.
Note that, both \code{rotateImg()} and \code{mirrorImg()} operate
on the \code{raster} matrix of the input \code{SpatialImage}.
Thus, any \code{SpatialImage} will automatically be coerced
into a \code{LoadedSpatialImage} upon rotation/mirroring.
}
\section{Other methods}{
\code{dim(x)} will return an integer vector of length 2,
containing the width and height of the image in pixels.
Note that this calls \code{imgRaster} under the hood and thus
may interact with the file and memory caches as described above.
For any \code{SpatialImage x}, \code{as(x, "LoadedSpatialImage")} will
create a \code{LoadedSpatialImage} containing an in-memory raster object.
For a \code{RemoteSpatialImage x}, \code{as(x, "StoredSpatialImage")} will
create a \code{StoredSpatialImage} pointing to the file cache location.
}
\examples{
path <- system.file(
"extdata", "10xVisium", "section1", "outs", "spatial",
"tissue_lowres_image.png", package="SpatialExperiment")
spi <- SpatialImage(path)
plot(imgRaster(spi))
# the following operations all use the cache
# so there is no need to reload the image
nrow(spi)
ncol(spi)
plot(as.raster(spi))
# coercing to an explicitly in-memory raster
spi <- as(spi, "LoadedSpatialImage")
plot(as.raster(spi))
###################
# transformations #
###################
# (counter-)clockwise rotation
spi1 <- rotateImg(spi, degrees = +90)
spi2 <- rotateImg(spi, degrees = -90)
par(mfrow = c(1, 3))
plot(as.raster(spi))
plot(as.raster(spi1))
plot(as.raster(spi2))
# horizontal/vertical mirroring
spi1 <- mirrorImg(spi, axis = "h")
spi2 <- mirrorImg(spi, axis = "v")
par(mfrow = c(1, 3))
plot(as.raster(spi))
plot(as.raster(spi1))
plot(as.raster(spi2))
}
\author{
Aaron Lun
}
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