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### =========================================================================
### realize()
### -------------------------------------------------------------------------
###
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Internal helper to support block by block realization
###
### Used by coercion to RleArray, HDF5Array::writeHDF5Array(), and
### HDF5Array::writeTENxMatrix().
###
BLOCK_write_to_sink <- function(x, sink)
{
stopifnot(identical(dim(x), dim(sink)))
## 'x' and 'sink' might both have their physical chunks but we must
## choose a grid that is compatible with the physical chunks of 'sink'.
## Calling 'blockGrid()' on 'sink' will produce such grid.
## Note that it might be beneficial to use a grid that is also compatible
## with the physical chunks of 'x' so we might want to come up with a
## dedicated utility for that e.g. 'blockGrid2(sink, x)'.
## Also by using block.shape="first-dim-grows-first" in the call below
## we'll get a grid that guarentees linear writing to the sink in case
## 'chunkdim(sink)' is NULL.
grid <- blockGrid(sink, block.shape="first-dim-grows-first")
nblock <- length(grid)
x_is_sparse <- is_sparse(x)
for (b in seq_len(nblock)) {
viewport <- grid[[b]]
if (x_is_sparse) {
if (get_verbose_block_processing())
message("Realizing sparse block ", b, "/", nblock, " ... ",
appendLF=FALSE)
sparse_block <- read_sparse_block(x, viewport)
if (get_verbose_block_processing())
message("OK, writing it ... ",
appendLF=FALSE)
write_sparse_block(sink, viewport, sparse_block)
if (get_verbose_block_processing())
message("OK")
} else {
if (get_verbose_block_processing())
message("Realizing block ", b, "/", nblock, " ... ",
appendLF=FALSE)
block <- read_block(x, viewport)
if (get_verbose_block_processing())
message("OK, writing it ... ",
appendLF=FALSE)
write_block(sink, viewport, block)
if (get_verbose_block_processing())
message("OK")
}
}
sink
}
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### realize()
###
setGeneric("realize", function(x, ...) standardGeneric("realize"))
setMethod("realize", "ANY",
function(x, BACKEND=getRealizationBackend())
{
x <- DelayedArray(x)
if (is.null(BACKEND))
return(DelayedArray(as.array(x)))
load_BACKEND_package(BACKEND)
ans <- as(x, BACKEND)
## Temporarily needed because coercion to HDF5Array currently drops
## the dimnames. See R/writeHDF5Array.R in the HDF5Array package for
## more information about this.
## TODO: Remove line below when this is addressed.
set_dimnames(ans, dimnames(x))
}
)
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