OME-ZARR Reader

NAMESPACE

@@ -4,6 +4,7 @@ S3method(as.raster,ImageArray)
 export(BFArray)
 export(BFPath)
 export(ImageArray)
+export(OZPath)
 export(createImageArray)
 export(getImageInfo)
 export(writeImageArray)
@@ -48,14 +49,20 @@ importFrom(EBImage,
   rotate
 )
 importFrom(HDF5Array,writeHDF5Array)
-importFrom(Rarr,write_zarr_group)
+importFrom(Rarr,
+  write_zarr_group,
+  zarr_overview
+)
 importFrom(S4Arrays,as.array.Array)
 importFrom(S4Vectors,
   SimpleList,
   coolcat,
   new2
 )
-importFrom(ZarrArray,writeZarrArray)
+importFrom(ZarrArray,
+  ZarrArray,
+  writeZarrArray
+)
 importFrom(grDevices,
   as.raster,
   rgb

R/AllClasses.R

@@ -6,18 +6,41 @@ NULL
 # magick classes
 setOldClass("magick-image")
 setOldClass("bitmap")
-setClassUnion(c("magick_class"), 
-              c("magick-image", "bitmap"))
 
 # array and matrix classes
-setClassUnion("matrix_array_Array", 
+setClassUnion("matrix_array_Array",
               c("matrix", "array", "Array"))
 
+#' @title ImageList class
+#'
+#' @description
+#' A \code{SimpleList} holding the levels of an \code{ImageArray} object.
+#'
+#' @keywords internal
+#' @noRd
 .ImageList <- setClass(
   Class="ImageList",
   contains="SimpleList",
   prototype=prototype(elementType="matrix_array_Array"))
 
+#' @title ImageArray class
+#'
+#' @description
+#' An S4 container for a multi-resolution (pyramidal) image, holding the
+#' pyramid levels together with their axis names and scales. Objects are
+#' created with \code{\link{ImageArray}}.
+#'
+#' @slot levels an \code{ImageList} of pyramid levels, ordered from the
+#'   highest to the lowest resolution
+#' @slot axes a character vector of axis names, a subset of
+#'   \code{c("c", "y", "x", "z", "t")}, of the same length as the number of
+#'   dimensions of every level
+#' @slot scales a list of named numeric vectors, one per level, where names
+#'   are a subset of \code{axes} and values are the scales of these axes. See
+#'   \url{https://ngff.openmicroscopy.org/} for more information. 
+#'
+#' @keywords internal
+#' @noRd
 .ImageArray <- setClass(
   Class = "ImageArray",
   slots = c(
@@ -27,15 +50,45 @@ setClassUnion("matrix_array_Array",
   )
 )
 
+#' @title BFPath class
+#'
+#' @description
+#' A pointer to a single series and resolutions of an image file read with
+#' \code{RBioFormats}, e.g. an OME-TIFF or a QPTIFF. Objects are created with
+#' \code{\link{BFPath}}.
+#'
+#' @slot filepath the path to the image read by \code{RBioFormats}
+#' @slot series the series ID of the pyramidal image, a single integer
+#'   typically starting from 1
+#' @slot resolution the resolution IDs of the pyramidal image, integers
+#'   typically starting from 1
+#'
+#' @keywords internal
+#' @noRd
 .BFPath <- setClass(
   Class = "BFPath",
   slots = c(
-    filepath = "character", 
+    filepath = "character",
     series = "numeric",
     resolution = "numeric"
   )
 )
 
+#' @title BFArraySeed class
+#'
+#' @description
+#'  The \code{DelayedArray} seed backing a \code{BFArray}. It extends
+#' \code{BFPath}, hence it also carries the \code{filepath}, \code{series} and
+#' \code{resolution} slots pointing to the image on disk.
+#'
+#' @slot axes a character vector of upper case axis names of the selected
+#'   series and resolution.
+#' @slot dim the dimension lengths of the selected series and resolution,
+#'   matching \code{axes}
+#' @slot type the storage type reported to \code{DelayedArray}.
+#'
+#' @keywords internal
+#' @noRd
 .BFArraySeed <- setClass(
   "BFArraySeed",
   contains = c("Array", "BFPath"),
@@ -46,8 +99,39 @@ setClassUnion("matrix_array_Array",
   )
 )
 
+#' @title BFArray class
+#'
+#' A \code{DelayedArray} giving lazy access to a single series and resolution
+#' of an image read with \code{RBioFormats}. Pixels are only read from disk
+#' when the array is realized. Objects are created with \code{\link{BFArray}}.
+#'
+#' @slot seed a \code{BFArraySeed} object
+#'
+#' @keywords internal
+#' @noRd
 .BFArray <- setClass(
   Class = "BFArray",
   contains = c("DelayedArray"),
   slots = c(seed = "BFArraySeed")
-)
+)
+
+#' @title OZPath class
+#'
+#' @description
+#' A pointer to the resolutions of an OME-Zarr store. Objects are created with
+#' \code{\link{OZPath}}.
+#'
+#' @slot filepath the path to the OME-Zarr store
+#' @slot resolution the names of the resolution directories of the pyramidal
+#'   image, e.g. "s0". Subdirectories of the store that are not zarr arrays,
+#'   such as the OME-NGFF "labels" group, are never resolutions
+#'
+#' @keywords internal
+#' @noRd
+.OZPath <- setClass(
+  Class = "OZPath",
+  slots = c(
+    filepath = "character",
+    resolution = "character"
+  )
+)