blockGrid {DelayedArray} | R Documentation |
blockGrid()
is the primary utility function to use to define a grid
that is suitable for block processing of an array-like object.
rowGrid()
and colGrid()
are additional functions, specific
to the 2-dimensional case. They can be used to define blocks of full rows
or full columns.
A family of utilities is provided to control the automatic block size (or length) and shape.
## Define grids to use in the context of block processing: blockGrid(x, block.length=NULL, chunk.grid=NULL, block.shape=NULL) rowGrid(x, nrow=NULL, block.length=NULL) colGrid(x, ncol=NULL, block.length=NULL) ## Control the automatic block size (or length) and shape: getAutoBlockSize() setAutoBlockSize(size=1e8) getAutoBlockLength(type) getAutoBlockShape() setAutoBlockShape(shape=c("hypercube", "scale", "first-dim-grows-first", "last-dim-grows-first"))
x |
An array-like or matrix-like object for A matrix-like object for |
block.length |
The length of the blocks i.e. the number of array elements per block.
By default the automatic block length (returned by
|
chunk.grid |
The grid of physical chunks.
By default |
block.shape |
A string specifying the shape of the blocks.
See |
nrow |
The number of rows of the blocks. The bottommost blocks might have less. See examples below. |
ncol |
The number of columns of the blocks. The rightmost blocks might have less. See examples below. |
size |
The automatic block size in bytes. Note that, except when the type of
the array data is The automatic block size is set to 100 Mb at package startup and can
be reset anytime to this value by calling |
type |
A string specifying the type of the array data. |
shape |
A string specifying the automatic block shape.
See The automatic block shape is set to |
By default, primary block processing functions blockApply()
and blockReduce()
use the grid returned by blockGrid(x)
to process array-like object x
block by block. This can be changed
with setAutoGridMaker()
.
See ?setAutoGridMaker
for more information.
blockGrid
: An ArrayGrid object on reference array x
.
The grid elements define the blocks that will be used to process x
by block. The grid is optimal in the sense that:
It's compatible with the grid of physical chunks a.k.a.
chunk grid. This means that, when the chunk grid is known
(i.e. when chunkGrid(x)
is not NULL or
chunk.grid
is supplied), every block in the grid contains
one or more full chunks. In other words, chunks never cross
block boundaries.
Its resolution is such that the blocks have a length
that is as close as possibe to (but does not exceed)
block.length
. An exception is made when some chunks
already have a length that is >= block.length
, in which
case the returned grid is the same as the chunk grid.
Note that the returned grid is regular (i.e. is a RegularArrayGrid object) unless the chunk grid is not regular (i.e. is an ArbitraryArrayGrid object).
rowGrid
: A RegularArrayGrid object on reference array x
where the grid elements define blocks made of full rows of x
.
colGrid
: A RegularArrayGrid object on reference array x
where the grid elements define blocks made of full columns of x
.
getAutoBlockSize
: The current automatic block size in bytes
as a single numeric value.
setAutoBlockSize
: The new automatic block size in bytes as an
invisible single numeric value.
getAutoBlockLength
: The automatic block length as a single integer
value.
getAutoBlockShape
: The current automatic block shape as a
single string.
setAutoBlockShape
: The new automatic block shape as an invisible
single string.
blockApply
and family to process an array-like
object block by block.
ArrayGrid objects.
The makeCappedVolumeBox
utility to make
capped volume boxes.
Advanced users: RealizationSink objects for writing an array-like object block by block to disk (or to memory).
## --------------------------------------------------------------------- ## A VERSION OF sum() THAT USES BLOCK PROCESSING ## --------------------------------------------------------------------- block_sum <- function(a, grid) { sums <- lapply(grid, function(viewport) sum(read_block(a, viewport))) sum(unlist(sums)) } ## On an ordinary matrix: m <- matrix(runif(600), ncol=12) m_grid <- blockGrid(m, block.length=120) sum1 <- block_sum(m, m_grid) sum1 ## On a DelayedArray object: library(HDF5Array) M <- as(m, "HDF5Array") sum2 <- block_sum(M, m_grid) sum2 sum3 <- block_sum(M, colGrid(M, block.length=120)) sum3 sum4 <- block_sum(M, rowGrid(M, block.length=80)) sum4 ## Sanity checks: sum0 <- sum(m) stopifnot(identical(sum1, sum0)) stopifnot(identical(sum2, sum0)) stopifnot(identical(sum3, sum0)) stopifnot(identical(sum4, sum0)) ## --------------------------------------------------------------------- ## blockGrid() ## --------------------------------------------------------------------- grid <- blockGrid(m, block.length=120) grid as.list(grid) # turn the grid into a list of ArrayViewport objects table(lengths(grid)) stopifnot(maxlength(grid) <= 120) grid <- blockGrid(m, block.length=120, block.shape="first-dim-grows-first") grid table(lengths(grid)) stopifnot(maxlength(grid) <= 120) grid <- blockGrid(m, block.length=120, block.shape="last-dim-grows-first") grid table(lengths(grid)) stopifnot(maxlength(grid) <= 120) blockGrid(m, block.length=100) blockGrid(m, block.length=75) blockGrid(m, block.length=25) blockGrid(m, block.length=20) blockGrid(m, block.length=10) ## --------------------------------------------------------------------- ## rowGrid() AND colGrid() ## --------------------------------------------------------------------- rowGrid(m, nrow=10) # 5 blocks of 10 rows each rowGrid(m, nrow=15) # 3 blocks of 15 rows each plus 1 block of 5 rows colGrid(m, ncol=5) # 2 blocks of 5 cols each plus 1 block of 2 cols ## See ?RealizationSink for an advanced example of user-implemented ## block processing using colGrid() and a realization sink. ## --------------------------------------------------------------------- ## CONTROL THE DEFAULT BLOCK SIZE (OR LENGTH) AND SHAPE ## --------------------------------------------------------------------- getAutoBlockSize() getAutoBlockLength("double") getAutoBlockLength("integer") getAutoBlockLength("logical") getAutoBlockLength("raw") setAutoBlockSize(140) getAutoBlockLength(type(m)) blockGrid(m) lengths(blockGrid(m)) dims(blockGrid(m)) getAutoBlockShape() setAutoBlockShape("scale") blockGrid(m) lengths(blockGrid(m)) dims(blockGrid(m)) ## Reset automatic block size and shape to factory settings: setAutoBlockSize() setAutoBlockShape()