address HG comments

Author: HelenaLC

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 ----
 

R/CTutils.R

@@ -220,7 +220,7 @@ setMethod("addCT", "SpatialDataAttrs", \(x, name, type="identity", data=NULL) {
         x[[ct]] <- new
     } else {
         switch( 
-            tryCatch(.zv(x), error=\(e) "9.9"), 
+            tryCatch(.ome_ver(x), error=\(e) "9.9"), 
             "0.3"=x$ome[[ms]][[1]][[ct]] <- new,
             x[[ms]][[1]][[ct]] <- new)
     }

R/sdArray.R

@@ -116,7 +116,7 @@ setMethod("data_type", "DelayedArray", \(x) {
 # internal use only!
 #' @noRd 
 .ch <- \(x) {
-    v <- tryCatch(.zv(x), error=\(e) NULL)
+    v <- tryCatch(.ome_ver(x), error=\(e) NULL)
     if (is.null(v)) return()
     if (v == "0.5") x <- x$ome
     unlist(x$omero$channels)

R/sdAttrs.R

@@ -126,21 +126,21 @@ setMethod("$", "SpatialDataAttrs", \(x, name) x[[name]])
 
 # internal use only!
 #' @noRd 
-.zv <- \(x) {
+.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 <- gsub("-.*", "", 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) {
-    v <- tryCatch(.zv(x), error=\(e) NULL)
+    v <- tryCatch(.ome_ver(x), error=\(e) NULL)
     if (is.null(v)) return()
     switch(v, "0.5"=x$ome$multiscales, x$multiscales)
 }