sdImage/Label and OME versioning (#249)

* fix sdattr versioning
* fix doc

Author: Artur-man

R/sdAttrs.R

@@ -61,7 +61,7 @@
 #' 
 #' @export
 SpatialDataAttrs <- \(x, type=c("image", "label", "frame"), 
-    trans=NULL, ver="0.4", dim=2, nch=3, ...) 
+    trans=NULL, ver="0.3", dim=2, nch=3, ...) 
 {
     stopifnot(
         length(dim) == 1, is.numeric(dim), dim %in% seq(2, 4),
@@ -72,16 +72,29 @@ SpatialDataAttrs <- \(x, type=c("image", "label", "frame"),
     ax <- .default_ax(type, dim)
     # transformations:
     ct <- trans %||% .default_ct(ax)
+    # datasets:
+    ds <- .default_ds(.ax_names(ax)) 
     # .zattrs list:
     if (type != "frame") {
         # default structure
-        res <- list(
-            omero=list(channels=list(label=letters[seq_len(nch)])),
-            multiscales=list(list(
-                axes=ax,
-                version="0.4",
-                coordinateTransformations=ct,
-                datasets=list(list(path="0", coordinateTransformations=list(list(type="scale", scale=list(1, 1))))))))
+        res <- list()
+        if(type != "label")
+          res <- c(res,
+                   list(omero=list(channels=lapply(letters[seq_len(nch)], 
+                                                   \(.) list(label = .)))))
+        res <- c(res,
+                 list(
+                   version=.get_ome_version(ver),
+                   multiscales=
+                     list(
+                       list(
+                         axes=ax,
+                         coordinateTransformations=ct,
+                         datasets=ds
+                       )
+                     )
+                 )
+        )
         if (ver == "0.3") res <- list(ome=res)
     } else {
         # points/shapes
@@ -120,13 +133,41 @@ SpatialDataAttrs <- \(x, type=c("image", "label", "frame"),
     return(ax)
 }
 
+# Internal helper to get axes names
+.ax_names <- function(ax){
+  if (is.character(ax[[1]])) {
+    unlist(ax)
+  } else {
+    vapply(ax, \(.) .$name, character(1))
+  }
+}
+
 # Internal helper to generate coordinate transformations
 .default_ct <- \(axes, name="global", type="identity", data=NULL) {
     ct <- list(input=axes, output=list(name=name), type=type)
     if (!is.null(data)) ct[[type]] <- data
     list(ct)
 }
 
+# Internal helper to generate datasets
+.default_ds <- function(axes, scale_factors = NULL){
+  scale_factors <- cumprod(c(1,scale_factors))
+  paths <- paste0(seq_along(scale_factors) - 1)
+  mapply(\(p,s) {
+    list(
+      coordinateTransformations = list(
+        list(
+          scale = lapply(
+            axes,
+            \(.) if(. == "c") 1 else s),
+          type = "scale"
+        )
+      ),
+      path = p
+    )
+  }, paths, scale_factors, USE.NAMES = FALSE, SIMPLIFY = FALSE)
+}
+
 #' @export
 #' @importFrom utils .DollarNames
 .DollarNames.SpatialDataAttrs <- \(x, pattern="") names(x)
@@ -147,6 +188,15 @@ setMethod("$", "SpatialDataAttrs", \(x, name) x[[name]])
     return(v)
 }
 
+.get_ome_version <- \(x){
+  switch(as.character(x), 
+         "0.1" = "0.4",
+         "0.2" = "0.4-dev-spatialdata",
+         "0.3" = "0.5-dev-spatialdata",
+         stop("Invalid SpatialDataImage/Label format! ", 
+              "Must be 0.1, 0.2, or 0.3"))
+}
+
 # internal use only!
 #' @noRd 
 setMethod("multiscales", "list", \(x) {