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Initial support for blockwise reader/iteration New classes: - `CoordsStrider`: new class to iterate through coordinate similar to Python's `_coords_strider` - `SOMASparseNDArrayReadBase`: base class for sparse array reads - `SOMASparseNDArrayBlockwiseRead`: new reader class for blockwise iterated reads New SOMA methods: - `SOMASparseNDArrayRead$blockwse()`: perform a blockwise read addresses #1853
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,129 @@ | ||
| CoordsStrider <- R6::R6Class( | ||
| classname = "CoordsStrider", | ||
| cloneable = FALSE, | ||
| public = list( | ||
| initialize = function(coords, ..., stride = NULL, start = NULL, end = NULL) { | ||
| if (missing(coords)) { | ||
| stopifnot( | ||
| rlang::is_integerish(start, 1L, TRUE) || | ||
| (inherits(start, "integer64") && length(start) == 1L && is.finite(start)), | ||
| rlang::is_integerish(end, 1L, TRUE) || | ||
| (inherits(end, "integer64") && length(end) == 1L && is.finite(end)), | ||
| start <= end | ||
| ) | ||
| private$.start <- start | ||
| private$.end <- end | ||
| stride <- stride %||% abs(end - start + 1L) | ||
| private$.index <- 0L | ||
| } else { | ||
| stopifnot(inherits(coords, c("integer64", "numeric", "integer"))) | ||
| private$.coords <- coords | ||
| stride <- stride %||% length(coords) | ||
| stopifnot(stride <= .Machine$integer.max) | ||
| private$.index <- 1L | ||
| } | ||
| stopifnot(rlang::is_integerish(stride, 1L, TRUE) && stride > 0L) | ||
| private$.stride <- stride | ||
| }, | ||
| print = function() { | ||
| cat("<", class(self)[1L], ">\n", sep = "") | ||
| if (is.null(self$coords)) { | ||
| cat(" start:", self$start, "\n") | ||
| cat(" end:", self$end, "\n") | ||
| } else { | ||
| cat(" length(coords):", length(self$coords), "\n") | ||
| } | ||
| cat(" stride:", self$stride, "\n") | ||
| return(invisible(self)) | ||
| }, | ||
| hasNext = function() { | ||
| if (is.null(self$coords)) { | ||
| return(private$.index <= abs(self$end - self$start)) | ||
| } | ||
| return(private$.index <= length(self$coords)) | ||
| }, | ||
| nextElem = function() { | ||
| if (!self$hasNext()) { | ||
| private$.stopIteration() | ||
| } | ||
| if (is.null(self$coords)) { | ||
| start <- min(self$start + private$.index, self$end) | ||
| end <- min(start + self$stride - 1L, self$end) | ||
| private$.index <- private$.index + self$stride | ||
| if (start == end) { | ||
| return(bit64::as.integer64(start)) | ||
| } | ||
| by <- ifelse(start <= end, 1L, -1L) | ||
| return(bit64::seq.integer64(from = start, to = end, by = by)) | ||
| } | ||
| start <- private$.index | ||
| end <- min(private$.index + self$stride - 1L, length(self$coords)) | ||
| private$.index <- end + 1 | ||
| return(self$coords[start:end]) | ||
| } | ||
| ), | ||
| active = list( | ||
| coords = function() private$.coords, | ||
| start = function() ifelse(is.null(self$coords), private$.start, min(self$coords)), | ||
| end = function() ifelse(is.null(self$coords), private$.end, max(self$coords)), | ||
| stride = function() private$.stride | ||
| ), | ||
| private = list( | ||
| .coords = NULL, | ||
| .start = NULL, | ||
| .end = NULL, | ||
| .stride = NULL, | ||
| .index = NULL, | ||
| .stopIteration = function() stop(errorCondition( | ||
| "StopIteration", | ||
| class = "stopIteration" | ||
| )) | ||
| ) | ||
| ) | ||
|
|
||
| #' @method as.list CoordsStrider | ||
| #' @export | ||
| #' | ||
| as.list.CoordsStrider <- function(x, ...) { | ||
| f <- get('as.list.iter', envir = asNamespace('iterators')) | ||
| return(f(x, ...)) | ||
| } | ||
|
|
||
| #' @importFrom iterators nextElem | ||
| #' @export | ||
| #' | ||
| iterators::nextElem | ||
|
|
||
| #' @method nextElem CoordsStrider | ||
| #' @export | ||
| #' | ||
| nextElem.CoordsStrider <- function(obj, ...) { | ||
| return(obj$nextElem()) | ||
| } | ||
|
|
||
| #' @importFrom itertools hasNext | ||
| #' @export | ||
| #' | ||
| itertools::hasNext | ||
|
|
||
| #' @method hasNext CoordsStrider | ||
| #' @export | ||
| #' | ||
| hasNext.CoordsStrider <- function(obj, ...) { | ||
| return(obj$hasNext()) | ||
| } | ||
|
|
||
| unlist64 <- function(x) { | ||
| stopifnot( | ||
| is.list(x), | ||
| all(vapply_lgl(x, inherits, what = 'integer64')) | ||
| ) | ||
| res <- bit64::integer64(sum(vapply_int(x, length))) | ||
| idx <- 1L | ||
| for (i in seq_along(x)) { | ||
| end <- idx + length(x[[i]]) | ||
| res[idx:(end - 1L)] <- x[[i]] | ||
| idx <- end | ||
| } | ||
| return(res) | ||
| } |
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