# Function to permute arrays of non-atomic elements (e.g. POSIXct)
.aperm2 <- function(x, new_order) {
  y <- array(1:length(x), dim = dim(x))
  y <- aperm(y, new_order)
  old_dims <- dim(x)
  x <- x[as.vector(y)]
  dim(x) <- old_dims[new_order]
  x
}

# Takes as input a list of arrays. The list must have named dimensions.
.MergeArrayOfArrays <- function(array_of_arrays) {
  MergeArrays <- startR:::.MergeArrays
  array_dims <- (dim(array_of_arrays))
  dim_names <- names(array_dims)

  # Merge the chunks.
  for (dim_index in 1:length(dim_names)) {
    dim_sub_array_of_chunks <- dim_sub_array_of_chunk_indices <- NULL
    if (dim_index < length(dim_names)) {
      dim_sub_array_of_chunks <- array_dims[(dim_index + 1):length(dim_names)]
      names(dim_sub_array_of_chunks) <- dim_names[(dim_index + 1):length(dim_names)]
      dim_sub_array_of_chunk_indices <- dim_sub_array_of_chunks
      sub_array_of_chunk_indices <- array(1:prod(dim_sub_array_of_chunk_indices),
                                          dim_sub_array_of_chunk_indices)
    } else {
      sub_array_of_chunk_indices <- NULL
    }
    sub_array_of_chunks <- vector('list', prod(dim_sub_array_of_chunks))
    dim(sub_array_of_chunks) <- dim_sub_array_of_chunks
    for (i in 1:prod(dim_sub_array_of_chunks)) {
      if (!is.null(sub_array_of_chunk_indices)) {
        chunk_sub_indices <- which(sub_array_of_chunk_indices == i, arr.ind = TRUE)[1, ]
      } else {
        chunk_sub_indices <- NULL
      }
      for (j in 1:(array_dims[dim_index])) {
        new_chunk <- do.call('[[', c(list(x = array_of_arrays),
                                     as.list(c(j, chunk_sub_indices))))
        #do.call('[[<-', c(list(x = array_of_chunks), 
        #                  as.list(c(j, chunk_sub_indices)),
        #                  list(value = NULL)))
        if (is.null(new_chunk)) {
          stop("Chunks missing.")
        }
        if (is.null(sub_array_of_chunks[[i]])) {
          sub_array_of_chunks[[i]] <- new_chunk
        } else {
          #if (length(new_chunk) != length(sub_array_of_chunks[[i]])) {
          #  stop("Missing components for some chunks.")
          #}
          #for (component in 1:length(new_chunk)) {
            sub_array_of_chunks[[i]] <- MergeArrays(sub_array_of_chunks[[i]],
                                                    new_chunk,
                                                    dim_names[dim_index])
          #}
        }
      }
    }
    array_of_arrays <- sub_array_of_chunks
    rm(sub_array_of_chunks)
    gc()
  }

  array_of_arrays[[1]]
}