S3 methods for as.array and bracket notation (#58)

Co-authored-by: PJ <52793278+pieterjanvc@users.noreply.github.com>

NAMESPACE

@@ -1,5 +1,9 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method("[",ZarrArray)
+S3method("[<-",ZarrArray)
+S3method(as.array,NestedArray)
+S3method(as.array,ZarrArray)
 export(Attributes)
 export(BloscCodec)
 export(Bz2Codec)

R/array-nested.R

@@ -299,7 +299,22 @@ NestedArray <- R6::R6Class("NestedArray",
         )
       }
       return(buf)
-
+    },
+    #' Convert NestArray object to R array (for S3 method)
+    #'
+    #' @return array
+    as.array = function() {
+      # Consider using drop() to simplify dimensions of 1
+      return(self$data)
     }
   )
 )
+
+#' S3 method for as.array
+#'
+#' @param obj 
+#' @keywords internal
+#' @export
+as.array.NestedArray = function(obj) {
+  obj$as.array()
+}

R/utils.R

@@ -289,4 +289,4 @@ get_list_product <- function(dim_indexer_iterables) {
     partial_results <- get_list_product_aux(dim_indexer_iterables, i, partial_results)
   }
   return(partial_results)
-}
+}

R/zarr-array.R

@@ -888,6 +888,100 @@ ZarrArray <- R6::R6Class("ZarrArray",
     },
     get_dimension_separator = function() {
       return(private$dimension_separator)
+    },
+    #' Set values for a selection using bracket notation (for S3 method).
+    #'
+    #' @param ... Contains the slicing parameters, one for each dimension.
+    #' Use empty space to get whole dimension e.g. [1:5,,]
+    #'
+    #' @return Sliced Zarr object
+    #' @keywords internal
+    `[` = function(...) {
+      filters <- substitute(...())
+      if(length(filters) != length(private$shape)) {
+        stop("This Zarr object has ", length(private$shape), " dimensions, ", length(filters), " were supplied")
+      }
+      filters <- lapply(filters, function(x) {
+        # Proceed based on type of filter
+        if(typeof(x) == "symbol") {
+          # When empty dimension, return everything
+          if(x == "") {
+            return(NULL)
+          } else {
+            stop("Unsupported filter '", as.character(x), "' supplied") 
+          }
+
+        } else if(typeof(x) == "double") {
+          # Return single value for dimension
+          return(slice(x, x))
+        } else if(typeof(x) == "language") {
+          x <- as.list(x)
+          # Return a range (supplied via : or seq())
+          if(x[[1]] == ":") {
+            return(slice(x[[2]], x[[3]]))
+          } else if(x[[1]] == "seq") {
+            arg_names <- names(x)
+            from <- ifelse("from" %in% arg_names, x[[which("from" == arg_names)]], x[[2]])
+            to <- ifelse("to" %in% arg_names, x[[which("to" == arg_names)]], x[[3]])
+            if(length(x) > 3) {
+              stop("Slicing with step size is not supported yet")
+              by <- ifelse("by" %in% arg_names, x[[which("by" == arg_names)]], x[[4]])
+            } else {
+              by <- NA
+            }
+            return(slice(from, to, by))
+          } else if(x[[1]] == "c") {
+            stop("Custom vector slicing is not yet supported")
+            # return(eval(y))
+          } else {
+            stop("Unsupported filter '", as.character(x), "' supplied")
+          }
+        } else {
+          stop("Unsupported filter '", as.character(x), "' supplied")
+        }
+      })
+      return(self$get_item(filters))
+    },
+    #' Assign values for a selection using bracket notation (for S3 method).
+    #' @keywords internal
+    `[<-` = function(...) {
+      stop("Assignment using bracket notation is not yet supported - use set_item() directly")
+    },
+    #' Convert Zarr object to R array (for S3 method). Note that this loads all data into memory.
+    #'
+    #' @return array
+    as.array = function() {
+      return(self$get_item("...")$data)
     }
   )
 )
+
+
+#' S3 method for custom bracket subsetting
+#'
+#' @param obj 
+#' @param ...
+#' @keywords internal 
+#' @export
+`[.ZarrArray` <- function(obj, ...) {
+  obj$`[`(...)
+}
+
+#' S3 method for custom bracket assignment
+#'
+#' @param obj 
+#' @param ...
+#' @keywords internal 
+#' @export
+`[<-.ZarrArray` <- function(obj, ...) {
+  obj$`[<-`(...)
+}
+
+#' S3 method for as.array
+#'
+#' @param obj 
+#' @keywords internal
+#' @export
+as.array.ZarrArray = function(obj) {
+  obj$as.array()
+}