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### =========================================================================
### Manipulating an Nindex
### -------------------------------------------------------------------------
###
### Nothing in this file is exported.
###
### An Nindex is a "multidimensional subsetting index". It's represented as a
### list with one subscript per dimension in the array-like object to subset.
### NULL list elements in it are interpreted as missing subscripts, that is, as
### subscripts that run along the full extend of the corresponding dimension.
### Before an Nindex can be used in a call to `[`, `[<-`, `[[` or `[[<-`, the
### NULL list elements must be replaced with objects of class "name".
###
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Normalization of an Nindex
###
normalizeSingleBracketSubscript2 <- function(i, x_len, x_names=NULL)
{
## We support subsetting by an array-like subscript but only if the
## subscript is mono-dimensional, in which case we call as.vector() on
## it. This will possibly trigger its realization e.g. if it's a
## DelayedArray object.
i_dim <- dim(i)
if (!is.null(i_dim)) {
if (length(i_dim) != 1L)
stop(wmsg("subsetting a DelayedArray object with an array-like ",
"subscript is only supported if the subscript has a ",
"single dimension"))
i <- as.vector(i)
}
## We create an artificial object 'x' of length 'x_len' with 'x_names' on
## it. normalizeSingleBracketSubscript() will only look at its length and
## names so what the object really is doesn't matter. Hence we make it
## with the smallest possible memory footprint.
## TODO: Change the signature of normalizeSingleBracketSubscript() in
## S4Vectors to take 'x_len' and 'x_names' instead of 'x' so we won't
## have to use this kind of trick.
if (is.null(x_names)) {
x <- Rle(0L, x_len)
} else {
x <- setNames(raw(x_len), x_names)
}
normalizeSingleBracketSubscript(i, x)
}
### Normalize 'Nindex' i.e. check and turn each non-NULL list element
### into a positive integer vector that is a valid subscript along the
### corresponding dimension in 'x'.
normalizeNindex <- function(Nindex, x)
{
x_dim <- dim(x)
if (is.null(x_dim))
stop(wmsg("'x' must be an array-like object"))
x_ndim <- length(x_dim)
if (is.null(Nindex))
return(vector("list", length=x_ndim))
if (!(is.list(Nindex) && length(Nindex) == x_ndim))
stop(wmsg("'Nindex' must be a list with one ",
"list element per dimension in 'x'"))
x_dimnames <- dimnames(x)
lapply(seq_len(x_ndim),
function(along) {
subscript <- Nindex[[along]]
if (is.null(subscript))
return(NULL)
d <- x_dim[[along]]
i <- normalizeSingleBracketSubscript2(subscript, d,
x_dimnames[[along]])
if (isSequence(i, of.length=d))
return(NULL)
i
})
}
### Assume 'Nindex' is normalized (see above).
### Return a logical vector with one logical per dimension indicating
### whether the corresponding subscript in 'Nindex' reaches all valid
### positions along the dimension.
subscript_has_nogap <- function(Nindex, dim)
{
stopifnot(is.list(Nindex), length(Nindex) == length(dim))
vapply(seq_along(Nindex),
function(along) {
Li <- Nindex[[along]]
if (is.null(Li))
return(TRUE)
d <- dim[[along]]
if (length(Li) < d)
return(FALSE)
hits <- logical(d)
hits[Li] <- TRUE
all(hits)
},
logical(1L),
USE.NAMES=FALSE)
}
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Other Nindex utilities
###
### For use in "[", "[<-", "[[", or "[[<-" methods to extract the user
### supplied subscripts as an Nindex. NULL subscripts are replace with
### integer(0). Missing subscripts are set to NULL.
extract_Nindex_from_syscall <- function(call, eframe)
{
Nindex <- lapply(seq_len(length(call) - 2L),
function(i) {
subscript <- call[[2L + i]]
if (missing(subscript))
return(NULL)
subscript <- eval(subscript, envir=eframe, enclos=eframe)
if (is.null(subscript))
return(integer(0))
subscript
}
)
argnames <- tail(names(call), n=-2L)
if (!is.null(argnames))
Nindex <- Nindex[!(argnames %in% c("drop", "exact", "value"))]
if (length(Nindex) == 1L && is.null(Nindex[[1L]]))
Nindex <- Nindex[0L]
Nindex
}
### Used in HDF5Array!
expand_Nindex_RangeNSBS <- function(Nindex)
{
stopifnot(is.list(Nindex))
expand_idx <- which(vapply(Nindex, is, logical(1), "RangeNSBS"))
if (length(expand_idx) != 0L)
Nindex[expand_idx] <- lapply(Nindex[expand_idx], as.integer)
Nindex
}
.make_subscripts_from_Nindex <- function(Nindex, x)
{
stopifnot(is.list(Nindex), length(Nindex) == length(dim(x)))
if (is.array(x))
Nindex <- expand_Nindex_RangeNSBS(Nindex)
## Replace NULLs with list elements of class "name".
subscripts <- rep.int(list(quote(expr=)), length(Nindex))
names(subscripts) <- names(Nindex)
not_missing_idx <- which(!S4Vectors:::sapply_isNULL(Nindex))
subscripts[not_missing_idx] <- Nindex[not_missing_idx]
subscripts
}
subset_by_Nindex <- function(x, Nindex, drop=FALSE)
{
subscripts <- .make_subscripts_from_Nindex(Nindex, x)
do.call(`[`, c(list(x), subscripts, list(drop=drop)))
}
### Return the modified array.
replace_by_Nindex <- function(x, Nindex, value)
{
subscripts <- .make_subscripts_from_Nindex(Nindex, x)
do.call(`[<-`, c(list(x), subscripts, list(value=value)))
}
subset_dimnames_by_Nindex <- function(dimnames, Nindex)
{
stopifnot(is.list(Nindex))
if (is.null(dimnames))
return(NULL)
ndim <- length(Nindex)
stopifnot(is.list(dimnames), length(dimnames) == ndim)
## Would mapply() be faster here?
ans <- lapply(setNames(seq_len(ndim), names(dimnames)),
function(along) {
dn <- dimnames[[along]]
i <- Nindex[[along]]
if (is.null(dn) || is.null(i))
return(dn)
extractROWS(dn, i)
})
simplify_NULL_dimnames(ans)
}
### Used in HDF5Array!
### Return the lengths of the subscripts in 'Nindex'. The length of a
### missing subscript is the length it would have after expansion.
get_Nindex_lengths <- function(Nindex, dim)
{
stopifnot(is.list(Nindex), length(Nindex) == length(dim))
ans <- lengths(Nindex)
missing_idx <- which(S4Vectors:::sapply_isNULL(Nindex))
ans[missing_idx] <- dim[missing_idx]
ans
}
### Convert 'Nindex' to a "linear index".
### Return the "linear index" as an integer vector if prod(dim) <=
### .Machine$integer.max, otherwise as a vector of doubles.
to_linear_index <- function(Nindex, dim)
{
stopifnot(is.list(Nindex), is.integer(dim), length(Nindex) == length(dim))
if (prod(dim) <= .Machine$integer.max) {
ans <- p <- 1L
} else {
ans <- p <- 1
}
for (along in seq_along(Nindex)) {
d <- dim[[along]]
i <- Nindex[[along]]
if (is.null(i))
i <- seq_len(d)
ans <- rep((i - 1L) * p, each=length(ans)) + ans
p <- p * d
}
ans
}
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