use BiocGenerics::data

DESCRIPTION

@@ -26,39 +26,14 @@ Authors@R: c(
     person("Vince", "Carey",
         role=c("aut"),
         email="stvjc@channing.harvard.edu",
-        comment=c(ORCID="0000-0003-4046-0063")),
-    person("Charlotte", "Soneson",
-        role=c("aut"),
-        email="charlotte.soneson@fmi.ch",
-        comment=c(ORCID="0000-0003-3833-2169")),
-    person("Michael", "Stadler",
-        role=c("aut"),
-        email="michael.stadler@fmi.ch",
-        comment=c(ORCID="0000-0002-2269-4934")),
-    person("Samuel", "Gunz",
-        role=c("aut"),
-        email="samuel.gunz@uzh.ch",
-        comment=c(ORCID="0000-0002-8909-0932")),
-    person("Yixing E.", "Dong",
-        role=c("aut"),
-        email="estelladong729@gmail.com",
-        comment=c(ORCID="0009-0003-5115-5686")),
-    person("Dario", "Righelli", 
-        role=c("aut"), 
-        email="dario.righelli@gmail.com",
-        comment=c(ORCID="0000-0003-1504-3583")),
-    person("Louise", "Deconinck",
-        role=c("aut"),
-        email="louise.deconinck@gmail.com",
-        comment=c(ORCID="0000-0001-8100-6823")))
+        comment=c(ORCID="0000-0003-4046-0063")))
 Imports:
     anndataR (>= 1.1.3),
     BiocGenerics,
     DBI,
     DelayedArray,
     dplyr,
     duckspatial,
-    EBImage,
     graph,
     Matrix,
     methods,
@@ -73,8 +48,8 @@ Imports:
     ZarrArray
 Suggests:
     BiocStyle,
+    EBImage,
     knitr,
-    paws,
     Rgraphviz,
     testthat
 biocViews: 

NAMESPACE

@@ -115,12 +115,15 @@ exportMethods(translation)
 importFrom(BiocGenerics,as.data.frame)
 importFrom(BiocGenerics,colnames)
 importFrom(BiocGenerics,combine)
+importFrom(BiocGenerics,data)
+importFrom(BiocGenerics,rotate)
 importFrom(BiocGenerics,rownames)
+importFrom(BiocGenerics,scale)
+importFrom(BiocGenerics,sequence)
 importFrom(BiocGenerics,table)
 importFrom(BiocGenerics,transform)
 importFrom(DBI,dbIsValid)
 importFrom(DelayedArray,DelayedArray)
-importFrom(EBImage,rotate)
 importFrom(Matrix,sparseMatrix)
 importFrom(Matrix,sparseVector)
 importFrom(Matrix,summary)
@@ -131,7 +134,6 @@ importFrom(Rarr,zarr_overview)
 importFrom(S4Vectors,"metadata<-")
 importFrom(S4Vectors,DataFrame)
 importFrom(S4Vectors,coolcat)
-importFrom(S4Vectors,isSequence)
 importFrom(S4Vectors,make_zero_col_DFrame)
 importFrom(S4Vectors,metadata)
 importFrom(S4Vectors,setValidity2)

R/AllGenerics.R

@@ -57,14 +57,10 @@ setGeneric("CTgraph", \(x, ...) standardGeneric("CTgraph"))
 setGeneric("rmvCT", \(x, ...) standardGeneric("rmvCT"))
 setGeneric("addCT", \(x, ...) standardGeneric("addCT"))
 
-setGeneric("scale", \(x, t, ...) standardGeneric("scale"))
-setGeneric("rotate", \(x, t, ...) standardGeneric("rotate"))
-setGeneric("sequence", \(x, t, ...) standardGeneric("sequence"))
-setGeneric("translation", \(x, t, ...) standardGeneric("translation"))
-
 setGeneric("flip", \(x, ...) standardGeneric("flip"))
 setGeneric("flop", \(x, ...) standardGeneric("flop"))
 setGeneric("mirror", \(x, ...) standardGeneric("mirror"))
+setGeneric("translation", \(x, t, ...) standardGeneric("translation"))
 
 # sda ----
 
@@ -83,11 +79,9 @@ setGeneric("instance_key<-", \(x, value) standardGeneric("instance_key<-"))
 
 # uts ----
 
-setGeneric("data", \(...) standardGeneric("data"))
 setGeneric("meta", \(x, ...) standardGeneric("meta"))
-
-setGeneric("data<-", \(x, ..., value) standardGeneric("data<-"))
 setGeneric("meta<-", \(x, ..., value) standardGeneric("meta<-"))
+setGeneric("data<-", \(x, ..., value) standardGeneric("data<-"))
 
 setGeneric("layer", \(x, i, ...) standardGeneric("layer"))
 setGeneric("element", \(x, i, ...) standardGeneric("element"))

R/CTutils.R

@@ -219,7 +219,8 @@ setMethod("addCT", "SpatialDataAttrs", \(x, name, type="identity", data=NULL) {
     if (is.null(multiscales(x))) {
         x[[ct]] <- new
     } else {
-        switch(.zv(x), 
+        switch( 
+            tryCatch(.ome_ver(x), error=\(e) "9.9"), 
             "0.3"=x$ome[[ms]][[1]][[ct]] <- new,
             x[[ms]][[1]][[ct]] <- new)
     }

R/methods.R

@@ -27,15 +27,10 @@ setMethod("[[", c("SpatialData", "character"), \(x, i, ...) attr(x, i))
 
 #' @export
 #' @rdname SpatialData
-setMethod("data", "ANY", \(...) {
-    l <- list(...)
-    x <- l[[1]]
-    if (!is(x, "SpatialDataElement")) 
-        return(utils::data(...))
-    if (!is(x, "SpatialDataArray")) 
-        return(x@data)
+#' @importFrom BiocGenerics data
+setMethod("data", "SpatialDataElement", \(x, k=1, ...) {
+    if (!is(x, "SpatialDataArray")) return(x@data)
     # return list of available scales
-    k <- if (length(l) == 1) 1 else l[[2]]
     if (is.null(k)) return(x@data)
     # should be a scalar positive integer
     ok <- length(k) == 1 && is.numeric(k) && k > 0 && k == round(k)

R/sdArray.R

@@ -116,7 +116,9 @@ setMethod("data_type", "DelayedArray", \(x) {
 # internal use only!
 #' @noRd 
 .ch <- \(x) {
-    if (.zv(x) == "0.3") x <- x$ome
+    v <- tryCatch(.ome_ver(x), error=\(e) NULL)
+    if (is.null(v)) return()
+    if (v == "0.5") x <- x$ome
     unlist(x$omero$channels)
 }
 
@@ -133,12 +135,12 @@ setMethod("channels", "SpatialDataImage", \(x, ...) channels(meta(x)))
 setMethod("channels", "SpatialDataElement", \(x, ...) stop("only 'images' have channels"))
 
 # compares metadata dataset paths to arrays on disk
-#' @importFrom S4Vectors isSequence
 .validate_multiscales_paths <- function(x, ds) {
     ps <- list.files(x)
     ds <- ds[ds %in% ps]
     if (!length(ds))
-      stop("Invalid SpatialData image or label: metadata does not match the names of Zarr arrays")
+        stop("Invalid 'SpatialData' image or label:",
+            " metadata does not match the names of Zarr arrays")
     return(ds)
 }
 

R/sdAttrs.R

@@ -126,17 +126,24 @@ setMethod("$", "SpatialDataAttrs", \(x, name) x[[name]])
 
 # internal use only!
 #' @noRd 
-.zv <- \(x) {
-    v <- x$spatialdata_attrs$version
+.ome_ver <- \(x) {
+    v <- 
+        x$multiscales[[1]]$version %||%
+        x$omero$version %||% 
+        x$ome$version
     if (!length(v)) stop("couldn't find 'version' in 'spatialdata_attrs'")
-    ok <- length(v) == 1 && is.character(v) && v %in% sprintf("0.%d", seq_len(5))
-    if (!ok) stop("invalid 'version' in 'spatialdata_attrs'; expected '0.x' where x is 1-5")
+    ok <- length(v) == 1 && is.character(v) && (v <- gsub("-.*", "", v)) %in% sprintf("0.%d", seq_len(6))
+    if (!ok) stop("invalid OME 'version'; expected '0.x' where x is 1-5")
     return(v)
 }
 
 # internal use only!
 #' @noRd 
-.ms <- \(x) switch(.zv(x), "0.3"=x$ome$multiscales, x$multiscales)
+.ms <- \(x) {
+    v <- tryCatch(.ome_ver(x), error=\(e) NULL)
+    if (is.null(v)) return()
+    switch(v, "0.5"=x$ome$multiscales, x$multiscales)
+}
 
 # internal use only!
 #' @noRd 

R/trans.R

@@ -48,9 +48,9 @@
 #' y["shapes", c("rot", "wide", "left")]
 NULL
 
-#' @importFrom BiocGenerics transform
 #' @export
 #' @rdname trans
+#' @importFrom BiocGenerics transform
 setMethod("transform", "SpatialDataElement", \(x, i=1, ...) {
     stopifnot(
         length(i) == 1, is.character(i) | 
@@ -70,7 +70,8 @@ setMethod("transform", "SpatialDataElement", \(x, i=1, ...) {
 
 #' @export
 #' @rdname trans
-setMethod("sequence", c("SpatialDataElement", "list"), \(x, t, ..., rev=FALSE) {
+#' @importFrom BiocGenerics sequence
+setMethod("sequence", "SpatialDataElement", \(x, t, ..., rev=FALSE) {
     if (rev) t <- rev(t)
     for (. in seq_along(t)) {
         if (is.null(t[[.]])) next
@@ -108,9 +109,11 @@ setMethod("flop", "SpatialDataArray", \(x, k=1, ...) .mirror(x, 90, k))
 #' @export
 #' @rdname trans
 #' @importFrom methods as
-#' @importFrom EBImage rotate
+#' @importFrom BiocGenerics rotate
 #' @importFrom S4Vectors metadata<-
-setMethod("rotate", c("SpatialDataArray", "numeric"), \(x, t, k=1, ..., rev=FALSE) {
+setMethod("rotate", "SpatialDataArray", \(x, t, k=1, ..., rev=FALSE) {
+    if (!requireNamespace("EBImage", quietly=TRUE))
+        stop("install 'EBImage' to use this function")
     # negate angle since 'EBImage' rotates clockwise
     stopifnot(length(t) == 1, is.finite(t))
     if (t %% 360 == 0) return(x)
@@ -151,8 +154,8 @@ setMethod("rotate", c("SpatialDataArray", "numeric"), \(x, t, k=1, ..., rev=FALS
 
 #' @export
 #' @rdname trans
-setMethod("scale", 
-    c("SpatialDataArray", "numeric"), 
+#' @importFrom BiocGenerics scale
+setMethod("scale", "SpatialDataArray",
     \(x, t, ...) .trans_a(x, t, "scale", ...))
 
 #' @export
@@ -204,14 +207,14 @@ setMethod("translation",
 
 #' @export
 #' @rdname trans
-setMethod("rotate", 
-    c("SpatialDataFrame", "numeric"), 
+#' @importFrom BiocGenerics rotate
+setMethod("rotate", "SpatialDataFrame",
     \(x, t, ...) .trans_f(x, t, "rotate", ...))
 
 #' @export
 #' @rdname trans
-setMethod("scale", 
-    c("SpatialDataFrame", "numeric"), 
+#' @importFrom BiocGenerics scale
+setMethod("scale", "SpatialDataFrame",
     \(x, t, ...) .trans_f(x, t, "scale", ...))
 
 #' @export

R/validity.R

@@ -49,10 +49,13 @@
 .validateImage <- \(object) {
     msg <- c()
     res <- length(object)
+    axs <- axes(object)
+    typ <- vapply(axs, \(.) .$type, character(1))
+    d <- sum(typ != "time")
     for (k in seq_len(res)) {
         x <- data(object, k)
-        if (length(dim(x)) != 3) msg <- c(msg, paste(
-            "'SpatialDataImage' resolution", k, "is not 3D"))
+        if (length(dim(x)) != d) msg <- c(msg, paste(
+            "'SpatialDataImage' resolution", k, "is not ", d, "D"))
         if (!type(x) %in% c("double", "integer")) msg <- c(msg, paste(
             "'SpatialDataImage' resolution", k, "is not of type double or integer"))
     }
@@ -65,10 +68,13 @@ setValidity2("SpatialDataImage", .validateImage)
 .validateLabel <- \(object) {
     msg <- c()
     res <- length(object)
+    axs <- axes(object)
+    typ <- vapply(axs, \(.) .$type, character(1))
+    d <- sum(typ == "space")
     for (k in seq_len(res)) {
         x <- data(object, k)
-        if (length(dim(x)) != 2) msg <- c(msg, paste(
-            "'SpatialDataLabel' resolution", k, "is not 2D"))
+        if (length(dim(x)) != d) msg <- c(msg, paste(
+            "'SpatialDataLabel' resolution", k, "is not ", d, "D"))
         if (type(x) != "integer") msg <- c(msg, paste(
             "'SpatialDataLabel' resolution", k, "is not of type integer"))
     }

inst/NEWS

@@ -1,6 +1,7 @@
 changes in version 0.99.38
 
-- use BiocGenerics::table
+- make use of new BiocGenerics:
+  data,rotate,scale,sequence,table,transform
 
 changes in version 0.99.37
 

tests/testthat/test-combine.R

@@ -4,7 +4,6 @@ x <- readSpatialData(x)
 
 test_that("combine", {
     # auto-fixed names
-    expect_error(combine(x))
     expect_no_message(y <- combine(x, x))
     f <- \(.) unlist(colnames(.))
     expect_all_true(f(x) %in% f(y))

tests/testthat/test-sdattrs.R

@@ -11,8 +11,6 @@ for (v in names(z)) {
         z <- multiscales(y)
         expect_is(z, "list")
         expect_length(z, 1)
-        y$spatialdata_attrs <- NULL
-        expect_error(multiscales(y))
     })
 
     test_that(paste0(v, "-axes"), {
@@ -48,4 +46,4 @@ for (v in names(z)) {
         expect_length(z, dim(y)[1])
     })
 
-}
+}