HistoImage
createHistoImage.Rd
Official constructor function of the S4 class HistoImage
. See
details for different input options of dir
and image
.
createHistoImage(
img_name,
sample,
dir = NULL,
img = NULL,
active = FALSE,
scale_factors = list(),
reference = FALSE,
verbose = TRUE,
...
)
Character value. The name of the HistoImage
with which
to refer to it via arguments img_name
and img_names
.
Character value. The sample name to which the image belongs.
Should be equal to slot @sample of the SpatialData
object in which
the HistoImage
is stored.
Character value. The directory from where to retrieve the image.
An image. Must be usable with EBImage::as.Image()
.
list. Sets slot @scale_factors,
Logical value. If TRUE
, the HistoImage
is
treated as the reference image for all other registered images in
the SpatialData
object.
Logical. If TRUE
, informative messages regarding
the computational progress will be printed.
(Warning messages will always be printed.)
Used to absorb deprecated arguments or functions.
An object of class HistoImage
The HistoImage
object stores the image as well as additional
information regarding the image. Among other things, it can store a file
directory. This, in turn, allows to conveniently use multiple images in
a SPATA2
object and in downstream analysis without having to store them
all together in the object which can occupy a lot of unnecessary memory
storage. The HistoImage
can be created in three ways.
First (recommended): The directory is specified via dir
and img
is NULL
.
In this case, the function reads the image from the directory and stores both,
the image as well as the directoryin the HistoImage
container. Since the
directory is stored, too, the image can be conveniently unloaded and loaded
in downstream analysis.
Second: The image is provided via img
and the directory dir
is NULL
.
In this case, the function creates the HistoImage
container and stores the
image but since no directory is available, unloading and loading later on
is not possible.
Third: Both, img
and dir
is specified. In this case, the image is stored
in the HistoImage
container next to the directory and if the directory dir
does not exist, the directory is used to save the image on the device which
allows unloading and loading later on.