SimpleList, path()

* use prototyped S4Vectors::SimpleList as slots
* new path() method to retrieve on-disk file paths
* more tests & validity
* bump to v0.99.39

Author: HelenaLC

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: spatialdataR
 Title: Representation of Python's spatialdata in R
 Depends: R (>= 4.6)
-Version: 0.99.38
+Version: 0.99.39
 Description: R interface to Python/scverse's 'spatialdata' framework for 
     unified spatial omics data handling. Adheres to OME-NGFF standards, 
     providing lazy, on-disk representations for multiscale images and 

NAMESPACE

@@ -91,6 +91,7 @@ exportMethods(mask)
 exportMethods(meta)
 exportMethods(mirror)
 exportMethods(names)
+exportMethods(path)
 exportMethods(point)
 exportMethods(pointNames)
 exportMethods(points)
@@ -116,6 +117,7 @@ importFrom(BiocGenerics,as.data.frame)
 importFrom(BiocGenerics,colnames)
 importFrom(BiocGenerics,combine)
 importFrom(BiocGenerics,data)
+importFrom(BiocGenerics,path)
 importFrom(BiocGenerics,rotate)
 importFrom(BiocGenerics,rownames)
 importFrom(BiocGenerics,scale)
@@ -133,6 +135,7 @@ importFrom(Rarr,read_zarr_attributes)
 importFrom(Rarr,zarr_overview)
 importFrom(S4Vectors,"metadata<-")
 importFrom(S4Vectors,DataFrame)
+importFrom(S4Vectors,SimpleList)
 importFrom(S4Vectors,coolcat)
 importFrom(S4Vectors,make_zero_col_DFrame)
 importFrom(S4Vectors,metadata)
@@ -167,6 +170,7 @@ importFrom(dplyr,select)
 importFrom(dplyr,slice)
 importFrom(dplyr,sql)
 importFrom(dplyr,tally)
+importFrom(dplyr,tibble)
 importFrom(duckspatial,as_duckspatial_df)
 importFrom(duckspatial,ddbs_bbox)
 importFrom(duckspatial,ddbs_create_conn)

R/AllClasses.R

@@ -1,16 +1,81 @@
+#' @importFrom S4Vectors SimpleList
 #' @importFrom methods setClass setClassUnion setOldClass
 
+.sdLayerList <- setClass(
+    Class="sdLayerList", 
+    contains="SimpleList", 
+    slots=c(metadata="list"),
+    prototype=prototype(metadata=list()))
+
+.sdImageList <- setClass(
+    Class="sdImageList",
+    contains="sdLayerList",
+    prototype=prototype(elementType="SpatialDataImage"))
+
+.sdLabelList <- setClass(
+    Class="sdLabelList",
+    contains="sdLayerList",
+    prototype=prototype(elementType="SpatialDataLabel"))
+
+.sdPointList <- setClass(
+    Class="sdPointList",
+    contains="sdLayerList",
+    prototype=prototype(elementType="SpatialDataPoint"))
+
+.sdShapeList <- setClass(
+    Class="sdShapeList",
+    contains="sdLayerList",
+    prototype=prototype(elementType="SpatialDataShape"))
+
+.sdTableList <- setClass(
+    Class="sdTableList",
+    contains="sdLayerList",
+    prototype=prototype(elementType="SingleCellExperiment"))
+
+.sl <- S4Vectors:::new_SimpleList_from_list
+.ok <- \(x) length(x) == 1L && (is.list(x[[1L]]) || is(x[[1L]], "SimpleList"))
+
+sdImageList <- \(...) {
+    x <- list(...)
+    if (.ok(x)) x <- x[[1L]]
+    .sl("sdImageList", as.list(x))
+}
+
+sdLabelList <- \(...) {
+    x <- list(...)
+    if (.ok(x)) x <- x[[1L]]
+    .sl("sdLabelList", as.list(x))
+}
+
+sdPointList <- \(...) {
+    x <- list(...)
+    if (.ok(x)) x <- x[[1L]]
+    .sl("sdPointList", as.list(x))
+}
+
+sdShapeList <- \(...) {
+    x <- list(...)
+    if (.ok(x)) x <- x[[1L]]
+    .sl("sdShapeList", as.list(x))
+}
+
+sdTableList <- \(...) {
+    x <- list(...)
+    if (.ok(x)) x <- x[[1L]]
+    .sl("sdTableList", as.list(x))
+}
+
 #' @export
 #' @rdname SpatialData
 .SpatialData <- setClass(
     Class="SpatialData",
     contains=c("list", "Annotated"),
     representation(
-        images="list",  # 'SpatialDataImage's
-        labels="list",  # 'SpatialDataLabel's
-        points="list",  # 'SpatialDataPoint's
-        shapes="list",  # 'SpatialDataShape's
-        tables="list")) # 'SingleCellExperiment's
+        images="sdImageList",
+        labels="sdLabelList",
+        points="sdPointList",
+        shapes="sdShapeList",
+        tables="sdTableList")) 
 
 .LAYERS <- `names<-`(. <- c("images","labels","points","shapes","tables"), .)
 .SpatialDataAttrs <- setClass("SpatialDataAttrs", contains="list")

R/CTutils.R

@@ -52,7 +52,7 @@ NULL
 #' @rdname CTutils
 #' @export
 setMethod("axes", "SpatialDataAttrs", \(x, ...) {
-    ms <- .ms(x)
+    ms <- multiscales(x)
     if (!is.null(ms)) x <- ms[[1]]
     if (is.null(x <- x$axes)) stop("couldn't find 'axes'") 
     return(x)
@@ -63,7 +63,7 @@ setMethod("axes", "SpatialDataAttrs", \(x, ...) {
 #' @rdname CTutils
 #' @export
 setMethod("CTlist", "SpatialDataAttrs", \(x, ...) {
-    ms <- .ms(x)
+    ms <- multiscales(x)
     ct <- "coordinateTransformations"
     if (is.null(ms)) return(x[[ct]])
     ms[[1]][[ct]]

R/SpatialData.R

@@ -53,13 +53,17 @@
 #' x[c(1, 2), list(1, c(1, 2))] # multiple
 #' 
 #' @export
-SpatialData <- \(images, labels, points, shapes, tables) {
-    if (missing(images)) images <- list()
-    if (missing(labels)) labels <- list()
-    if (missing(points)) points <- list()
-    if (missing(shapes)) shapes <- list()
-    if (missing(tables)) tables <- list()
+SpatialData <- \(
+    images=list(), 
+    labels=list(), 
+    points=list(), 
+    shapes=list(), 
+    tables=list())
+{
     .SpatialData(
-        images=images, labels=labels, 
-        points=points, shapes=shapes, tables=tables)
+        images=sdImageList(images),
+        labels=sdLabelList(labels),
+        points=sdPointList(points),
+        shapes=sdShapeList(shapes),
+        tables=sdTableList(tables))
 }