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|
### =========================================================================
### DelayedAbind objects
### -------------------------------------------------------------------------
###
### Representation of a delayed abind() operation.
###
setClass("DelayedAbind",
contains="DelayedNaryOp",
representation(
along="integer" # Single integer indicating the dimension along
# which to bind the input objects.
),
prototype(
along=1L
)
)
.validate_DelayedAbind <- function(x)
{
## 'along' slot.
if (!(isSingleInteger(x@along) && x@along >= 1L))
return("'x@along' must be a single positive integer")
ndim <- length(dim(x@seeds[[1L]]))
if (ndim < x@along)
return(paste0("the array-like objects to bind must have at least ",
x@along, " dimensions for this binding operation"))
dims <- get_dims_to_bind(x@seeds, x@along)
if (is.character(dims))
return(dims)
TRUE
}
setValidity2("DelayedAbind", .validate_DelayedAbind)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Constructor
###
new_DelayedAbind <- function(seeds, along)
{
new2("DelayedAbind", seeds=seeds, along=along)
}
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### is_noop() method
###
setMethod("is_noop", "DelayedAbind",
function(x) length(x@seeds) == 1L
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Display
###
### S3/S4 combo for summary.DelayedAbind
.DelayedAbind_summary <-
function(object) sprintf("Abind (along=%d)", object@along)
summary.DelayedAbind <-
function(object, ...) .DelayedAbind_summary(object, ...)
setMethod("summary", "DelayedAbind", summary.DelayedAbind)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Seed contract
###
.get_DelayedAbind_dim <- function(x)
{
dims <- get_dims_to_bind(x@seeds, x@along)
combine_dims_along(dims, x@along)
}
setMethod("dim", "DelayedAbind", .get_DelayedAbind_dim)
.get_DelayedAbind_dimnames <- function(x)
{
dims <- get_dims_to_bind(x@seeds, x@along)
combine_dimnames_along(x@seeds, dims, x@along)
}
setMethod("dimnames", "DelayedAbind", .get_DelayedAbind_dimnames)
.extract_array_from_DelayedAbind <- function(x, index)
{
i <- index[[x@along]]
if (is.null(i)) {
## This is the easy situation.
arrays <- lapply(x@seeds, extract_array, index)
## Bind the ordinary arrays in 'arrays'.
ans <- do.call(simple_abind, c(arrays, list(along=x@along)))
return(ans)
}
## From now on 'i' is a vector of positive integers.
dims <- get_dims_to_bind(x@seeds, x@along)
breakpoints <- cumsum(dims[x@along, ])
part_idx <- get_part_index(i, breakpoints)
split_part_idx <- split_part_index(part_idx, length(breakpoints))
FUN <- function(s) {
index[[x@along]] <- split_part_idx[[s]]
extract_array(x@seeds[[s]], index)
}
arrays <- lapply(seq_along(x@seeds), FUN)
## Bind the ordinary arrays in 'arrays'.
ans <- do.call(simple_abind, c(arrays, list(along=x@along)))
## Reorder the rows or columns in 'ans'.
Nindex <- vector("list", length=length(index))
Nindex[[x@along]] <- get_rev_index(part_idx)
extract_array(ans, Nindex)
}
setMethod("extract_array", "DelayedAbind", .extract_array_from_DelayedAbind)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Propagation of sparsity
###
setMethod("is_sparse", "DelayedAbind",
function(x)
{
all(vapply(x@seeds, is_sparse, logical(1), USE.NAMES=FALSE))
}
)
.extract_sparse_array_DelayedAbind <- function(x, index)
{
i <- index[[x@along]]
if (is.null(i)) {
## This is the easy situation.
arrays <- lapply(x@seeds, extract_sparse_array, index)
## Bind the SparseArraySeed objects in 'arrays'.
ans <- abind_SparseArraySeed_objects(arrays, x@along)
return(ans)
}
## From now on 'i' is a vector of positive integers.
dims <- get_dims_to_bind(x@seeds, x@along)
breakpoints <- cumsum(dims[x@along, ])
part_idx <- get_part_index(i, breakpoints)
split_part_idx <- split_part_index(part_idx, length(breakpoints))
FUN <- function(s) {
index[[x@along]] <- split_part_idx[[s]]
extract_sparse_array(x@seeds[[s]], index)
}
arrays <- lapply(seq_along(x@seeds), FUN)
## Bind the SparseArraySeed objects in 'arrays'.
ans <- abind_SparseArraySeed_objects(arrays, x@along)
## Reorder the rows or columns in 'ans'.
Nindex <- vector("list", length=length(index))
Nindex[[x@along]] <- get_rev_index(part_idx)
extract_sparse_array(ans, Nindex)
}
### 'is_sparse(x)' is assumed to be TRUE and 'index' is assumed to
### not contain duplicates. See "extract_sparse_array() Terms of Use"
### in SparseArraySeed-class.R
setMethod("extract_sparse_array", "DelayedAbind",
.extract_sparse_array_DelayedAbind
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Backward compatibility with DelayedArray < 0.5.24
###
### In DelayedArray 0.5.24 the SeedBinder class got renamed DelayedAbind.
### DelayedArray objects serialized with DelayedArray < 0.5.24 might contain
### SeedBinder instances nested in their "seed" slot so we need to keep
### the class around for now.
###
setClass("SeedBinder", contains="DelayedAbind")
setMethod("updateObject", "SeedBinder",
function(object, ..., verbose=FALSE)
{
class(object) <- "DelayedAbind"
callNextMethod()
}
)
|
