Style/comments

R/array-nested.R

@@ -300,11 +300,11 @@ NestedArray <- R6::R6Class("NestedArray",
       }
       return(buf)
     },
-    #' Convert NestArray object to R array
+    #' Convert NestArray object to R array (for S3 method)
     #'
     #' @return array
-    as.array = function(){
-      #Consider using drop() to simplify dimensions of 1
+    as.array = function() {
+      # Consider using drop() to simplify dimensions of 1
       return(self$data)
     }
   )
@@ -315,6 +315,6 @@ NestedArray <- R6::R6Class("NestedArray",
 #' @param obj 
 #' @keywords internal
 #' @export
-as.array.NestedArray = function(obj){
+as.array.NestedArray = function(obj) {
   obj$as.array()
 }

R/zarr-array.R

@@ -889,68 +889,69 @@ ZarrArray <- R6::R6Class("ZarrArray",
     get_dimension_separator = function() {
       return(private$dimension_separator)
     },
-    #' Subset / slice Zarr object using bracket notation
+    #' Set values for a selection using bracket notation (for S3 method).
     #'
     #' @param ... Contains the slicing parameters, one for each dimension.
     #' Use empty space to get whole dimension e.g. [1:5,,]
     #'
     #' @return Sliced Zarr object
+    #' @keywords internal
     `[` = function(...) {
-      filters = substitute(...())
-      if(length(filters) != length(private$shape)){
-        stop("This Zarr object has ",length(private$shape)," dimensions, ",
-             length(filters)," were supplied")
-      }
-      filters = lapply(filters, function(x){
-        #Proceed based on type of filter
-        if(typeof(x) == "symbol"){
-          #When empty dimension, return everything
-          if(x == ""){
+      filters <- substitute(...())
+      if(length(filters) != length(private$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
+        } 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]] == ":"){
+        } 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"){
-            argNames <- names(x)
-            from <- ifelse("from" %in% argNames, x[[which("from" == argNames)]], x[[2]])
-            to <- ifelse("to" %in% argNames, x[[which("to" == argNames)]], x[[3]])
-            if(length(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% argNames, x[[which("by" == argNames)]], x[[4]])
+              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 supported yet")
+          } else if(x[[1]] == "c") {
+            stop("Custom vector slicing is not yet supported")
             # return(eval(y))
-          } else{
+          } else {
             stop("Unsupported filter '", as.character(x), "' supplied")
           }
-
         } else {
           stop("Unsupported filter '", as.character(x), "' supplied")
         }
       })
-      return(self$get_basic_selection(filters))
+      return(self$get_item(filters))
     },
+    #' Assign values for a selection using bracket notation (for S3 method).
+    #' @keywords internal
     `[<-` = function(...) {
-      stop("Updating values using bracket subsetting is currently not possible")
+      stop("Assignment using bracket notation is not yet supported - use set_item() directly")
     },
-    #' Convert Zarr object to R array
+    #' Convert Zarr object to R array (for S3 method). Note that this loads all data into memory.
     #'
     #' @return array
-    as.array = function(){
-      return(self$get_basic_selection("...")$data)
+    as.array = function() {
+      return(self$get_item("...")$data)
     }
   )
 )
@@ -962,7 +963,7 @@ ZarrArray <- R6::R6Class("ZarrArray",
 #' @param ...
 #' @keywords internal 
 #' @export
-`[.ZarrArray` <- function(obj, ...){
+`[.ZarrArray` <- function(obj, ...) {
   obj$`[`(...)
 }
 
@@ -972,7 +973,7 @@ ZarrArray <- R6::R6Class("ZarrArray",
 #' @param ...
 #' @keywords internal 
 #' @export
-`[<-.ZarrArray` <- function(obj, ...){
+`[<-.ZarrArray` <- function(obj, ...) {
   obj$`[<-`(...)
 }
 
@@ -981,6 +982,6 @@ ZarrArray <- R6::R6Class("ZarrArray",
 #' @param obj 
 #' @keywords internal
 #' @export
-as.array.ZarrArray = function(obj){
+as.array.ZarrArray = function(obj) {
   obj$as.array()
 }