Generate automatic grids to use for block processing of array-like objects
defaultAutoGrid() is the default automatic grid maker.
It creates a grid that is suitable for block processing of the array-like
object passed to it.
rowAutoGrid() and colAutoGrid() are additional
automatic grid makers, specific to the 2-dimensional case.
They can be used to define blocks of full rows or full columns.
defaultAutoGrid(x, block.length=NULL, chunk.grid=NULL, block.shape=NULL) rowAutoGrid(x, nrow=NULL, block.length=NULL) colAutoGrid(x, ncol=NULL, block.length=NULL) ## Replace default automatic grid maker with user-defined one: getAutoGridMaker() setAutoGridMaker(GRIDMAKER="defaultAutoGrid")
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. |
GRIDMAKER |
The function to use as automatic grid maker, that is, the
function that will be used by
The automatic grid maker is set to |
By default, primary block processing functions blockApply()
and blockReduce() use the grid returned by
defaultAutoGrid(x) to process array-like object x
block by block. This can be changed with setAutoGridMaker().
defaultAutoGrid: 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).
rowAutoGrid: A RegularArrayGrid object on reference array
x where the grid elements define blocks made of full rows of x.
colAutoGrid: A RegularArrayGrid object on reference array
x where the grid elements define blocks made of full columns
of x.
setAutoBlockSize and setAutoBlockShape
to control the geometry of automatic blocks.
blockApply and family for convenient block
processing of an array-like object.
ArrayGrid for the formal representation of grids and viewports.
The makeCappedVolumeBox utility to make
capped volume boxes.
read_block and write_block.
## ---------------------------------------------------------------------
## 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 <- defaultAutoGrid(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, colAutoGrid(M, block.length=120))
sum3
sum4 <- block_sum(M, rowAutoGrid(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))
## ---------------------------------------------------------------------
## defaultAutoGrid()
## ---------------------------------------------------------------------
grid <- defaultAutoGrid(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 <- defaultAutoGrid(m, block.length=120,
block.shape="first-dim-grows-first")
grid
table(lengths(grid))
stopifnot(maxlength(grid) <= 120)
grid <- defaultAutoGrid(m, block.length=120,
block.shape="last-dim-grows-first")
grid
table(lengths(grid))
stopifnot(maxlength(grid) <= 120)
defaultAutoGrid(m, block.length=100)
defaultAutoGrid(m, block.length=75)
defaultAutoGrid(m, block.length=25)
defaultAutoGrid(m, block.length=20)
defaultAutoGrid(m, block.length=10)
## ---------------------------------------------------------------------
## rowAutoGrid() AND colAutoGrid()
## ---------------------------------------------------------------------
rowAutoGrid(m, nrow=10) # 5 blocks of 10 rows each
rowAutoGrid(m, nrow=15) # 3 blocks of 15 rows each plus 1 block of 5 rows
colAutoGrid(m, ncol=5) # 2 blocks of 5 cols each plus 1 block of 2 cols
## See '?write_block' for an advanced example of user-implemented
## block processing using colAutoGrid() and a realization sink.
## ---------------------------------------------------------------------
## REPLACE DEFAULT AUTOMATIC GRID MAKER WITH USER-DEFINED ONE
## ---------------------------------------------------------------------
getAutoGridMaker()
setAutoGridMaker(function(x) colAutoGrid(x, ncol=5))
getAutoGridMaker()
blockApply(m, function(block) currentViewport())
## Reset automatic grid maker to factory settings:
setAutoGridMaker()Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.