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### =========================================================================
### rowsum() and colsum() methods for DelayedMatrix objects
### -------------------------------------------------------------------------
###
### These methods are block processed.
###
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Simple helpers to support verbose operations
###
.summarize_matrix <- function(x)
{
ans <- paste0("<", paste0(dim(x), collapse=" x "), "> ", class(x)[[1L]])
if (is.object(x))
ans <- paste0(ans, " object")
ans
}
final_hstrip_noop <- function(init, i, grid) {
what <- .summarize_matrix(init)
#message(" ", wmsg("| result for horizontal strip ",
# i, "/", nrow(grid), ": ", what))
message(" ", wmsg("| result is a ", what, " --> returning as-is"))
init
}
final_vstrip_noop <- function(init, j, grid) {
what <- .summarize_matrix(init)
#message(" ", wmsg("| result for vertical strip ",
# j, "/", ncol(grid), ": ", what))
message(" ", wmsg("| result is a ", what, " --> returning as-is"))
init
}
realize_matrix <- function(x, BACKEND, verbose)
{
if (verbose) {
what <- .summarize_matrix(x)
message(" ", wmsg("| realizing ", what, " as ",
BACKEND, " object ..."),
" ", appendLF=FALSE)
}
ans <- realize(x, BACKEND=BACKEND)
if (verbose)
message("ok")
ans
}
write_full_sink_rows <- function(sink, sink_grid, i, block, verbose)
{
if (verbose) {
what <- .summarize_matrix(block)
message(" ", wmsg("| writing ", what, " to ",
class(sink), " object ..."),
" ", appendLF=FALSE)
}
sink <- write_block(sink, sink_grid[[i, 1L]], block)
if (verbose)
message("ok")
sink
}
write_full_sink_cols <- function(sink, sink_grid, j, block, verbose)
{
if (verbose) {
what <- .summarize_matrix(block)
message(" ", wmsg("| writing ", what, " to ",
class(sink), " object ..."),
" ", appendLF=FALSE)
}
sink <- write_block(sink, sink_grid[[1L, j]], block)
if (verbose)
message("ok")
sink
}
### 'strip_results' is guaranteed to be a list of length >= 1.
combine_strip_results <- function(fname, strip_results, verbose)
{
res1 <- strip_results[[1L]]
if (length(strip_results) == 1L)
return(res1)
if (verbose) {
message(wmsg("=== FINAL STEP ==="))
if (is.matrix(res1)) {
what <- "matrices"
} else {
what <- paste0(class(res1)[[1L]], " objects")
}
message(" ", wmsg("| ", fname, "()'ing strip results ",
"(", length(strip_results), " ", what, ") ",
"together ..."),
" ", appendLF=FALSE)
}
FUN <- match.fun(fname)
ans <- do.call(FUN, strip_results)
if (verbose) {
message("ok")
message("=== DONE ===\n")
}
ans
}
shared_sink_as_DelayedArray <- function(sink, verbose)
{
if (verbose) {
message(wmsg("=== FINAL STEP ==="))
message(" ", wmsg("| turning ", class(sink), " object ",
"into DelayedArray object ..."),
" ", appendLF=FALSE)
}
close(sink)
ans <- as(sink, "DelayedArray")
if (verbose) {
message("ok")
message("=== DONE ===\n")
}
ans
}
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Helpers for BLOCK_rowsum() and BLOCK_colsum()
###
### 'input_grid' must be a 2D grid.
### Returns a 2D grid 'sink_grid' that verifies:
### (a) refdim(sink_grid)[[1]] == refdim(input_grid)[[1]];
### (b) refdim(sink_grid)[[2]] == sink_ncol;
### (c) the blocks on 'sink_grid' are made of full rows and they align
### with the horizontal strips on 'input_grid'.
### The consequences of (c) are that ncol(sink_grid) == 1 and
### nrow(sink_grid) == length(sink_grid) == nrow(input_grid).
.make_sink_grid_of_hstrips <- function(input_grid, sink_ncol)
{
stopifnot(is(input_grid, "ArrayGrid"),
length(dim(input_grid)) == 2L,
isSingleInteger(sink_ncol))
if (is(input_grid, "ArbitraryArrayGrid")) {
tickmarks <- list(input_grid@tickmarks[[1L]], sink_ncol)
ArbitraryArrayGrid(tickmarks)
} else {
refdim <- c(refdim(input_grid)[[1L]], sink_ncol)
spacings <- c(nrow(input_grid[[1L]]), sink_ncol)
RegularArrayGrid(refdim, spacings=spacings)
}
}
### 'input_grid' must be a 2D grid.
### Returns a 2D grid 'sink_grid' that verifies:
### (a) refdim(sink_grid)[[1]] == sink_nrow;
### (b) refdim(sink_grid)[[2]] == refdim(input_grid)[[2]];
### (c) the blocks on 'sink_grid' are made of full columns and they align
### with the vertical strips on 'input_grid'.
### The consequences of (c) are that nrow(sink_grid) == 1 and
### ncol(sink_grid) == length(sink_grid) == ncol(input_grid).
.make_sink_grid_of_vstrips <- function(input_grid, sink_nrow)
{
stopifnot(is(input_grid, "ArrayGrid"),
length(dim(input_grid)) == 2L,
isSingleInteger(sink_nrow))
if (is(input_grid, "ArbitraryArrayGrid")) {
tickmarks <- list(sink_nrow, input_grid@tickmarks[[2L]])
ArbitraryArrayGrid(tickmarks)
} else {
refdim <- c(sink_nrow, refdim(input_grid)[[2L]])
spacings <- c(sink_nrow, ncol(input_grid[[1L]]))
RegularArrayGrid(refdim, spacings=spacings)
}
}
### Note that each block on 'sink_grid' is a horizontal strip made of one or
### more rows.
.sink_chunking_is_compatible_with_hstrips <- function(sink_chunkdim, sink_grid)
{
stopifnot(is(sink_grid, "ArrayGrid"),
length(dim(sink_grid)) == 2L,
ncol(sink_grid) == 1L)
if (is.null(sink_chunkdim)) # no-chunking
return(TRUE)
stopifnot(is.integer(sink_chunkdim), length(sink_chunkdim) == 2L)
## We treat the "single big chunk" case like the no-chunking case.
## Note that the "single big chunk" situation only happens for very
## small sinks in which case the chunking does not significantly impact
## the writing performance. However, treating this situation as compatible
## with horizontal sink strips is convenient when testing things like
## BLOCK_colsum(..., BACKEND="HDF5Array") on a small toy dataset.
if (all(sink_chunkdim == refdim(sink_grid)))
return(TRUE)
## Dumb heuristic: We consider incompatible chunks that are taller than
## the first block in 'sink_grid'.
## FIXME: This could certainly be improved/refined.
## Anyway, the most important thing for now is that it covers the
## worst-case scenario, which is when the sink uses a storage layout
## that is column-oriented (e.g. TENxRealizationSink object),
## and 'sink_grid' has more than one horizontal strip.
## So whatever heuristic we use, we want to make sure that it returns
## FALSE in this case.
if (sink_chunkdim[[1L]] <= nrow(sink_grid[[1L]]))
return(TRUE)
FALSE
}
### Note that each block on 'sink_grid' is a vertical strip made of one or
### more columns.
.sink_chunking_is_compatible_with_vstrips <- function(sink_chunkdim, sink_grid)
{
stopifnot(is(sink_grid, "ArrayGrid"),
length(dim(sink_grid)) == 2L,
nrow(sink_grid) == 1L)
if (is.null(sink_chunkdim)) # no-chunking
return(TRUE)
stopifnot(is.integer(sink_chunkdim), length(sink_chunkdim) == 2L)
if (all(sink_chunkdim == refdim(sink_grid)))
return(TRUE)
## Dumb heuristic: We consider incompatible chunks that are wider than
## the first block in 'sink_grid'.
## FIXME: This could certainly be improved/refined.
## Anyway, the most important thing for now is that it covers the
## worst-case scenario, which is when the sink uses a storage layout
## that is row-oriented (i.e. is the transposed of what is used by a
## TENxRealizationSink object), and 'sink_grid' has more than one
## vertical strip. Whatever heuristic we use, we want to make sure that
## it returns FALSE in this case.
if (sink_chunkdim[[2L]] <= ncol(sink_grid[[1L]]))
return(TRUE)
FALSE
}
### Whether 'BACKEND' is compatible with the "shared sink" route (see below
### in this file for what the "shared sink" route is).
.compatible_BACKEND <- function(BACKEND)
{
if (is.null(BACKEND))
return(FALSE)
## Same check as in load_BACKEND_package().
if (!isSingleString(BACKEND))
stop(wmsg("'BACKEND' must be a single string or NULL"))
## write_block() method for RleRealizationSink objects is broken (it
## ignores the 'viewport' argument!) so, until this is fixed, the
## RleArray realization backend is not compatible.
BACKEND != "RleArray"
}
### Returns a "shared sink" if we can take the "shared sink" route, or NULL if
### we can't. ALWAYS takes the "shared sink" route if 'nrow(input_grid)' is 1.
.make_shared_sink_along_hstrips <- function(input_grid, sink_grid, BACKEND,
sink_rownames, sink_colnames, ...)
{
stopifnot(nrow(sink_grid) == nrow(input_grid), ncol(sink_grid) == 1L)
if (nrow(input_grid) != 1L && !.compatible_BACKEND(BACKEND))
return(NULL)
sink_dimnames <- list(sink_rownames, sink_colnames)
sink <- RealizationSink(BACKEND, refdim(sink_grid), dimnames=sink_dimnames,
type="double", ...)
if (nrow(input_grid) == 1L)
return(sink)
## We take the "shared sink" route only if the chunks are "compatible"
## with the writing of full sink rows by callback function FINAL()
## below (this callback function will get called at the end of processing
## each horizontal strip).
ok <- .sink_chunking_is_compatible_with_hstrips(chunkdim(sink), sink_grid)
if (ok) sink else NULL
}
### Returns a "shared sink" if we can take the "shared sink" route, or NULL if
### we can't. ALWAYS takes the "shared sink" route if 'ncol(input_grid)' is 1.
.make_shared_sink_along_vstrips <- function(input_grid, sink_grid, BACKEND,
sink_rownames, sink_colnames, ...)
{
stopifnot(nrow(sink_grid) == 1L, ncol(sink_grid) == ncol(input_grid))
if (ncol(input_grid) != 1L && !.compatible_BACKEND(BACKEND))
return(NULL)
sink_dimnames <- list(sink_rownames, sink_colnames)
sink <- RealizationSink(BACKEND, refdim(sink_grid), dimnames=sink_dimnames,
type="double", ...)
if (ncol(input_grid) == 1L)
return(sink)
## We take the "shared sink" route only if the chunks are "compatible"
## with the writing of full sink columns by callback function FINAL()
## below (this callback function will get called at the end of processing
## each vertical strip).
ok <- .sink_chunking_is_compatible_with_vstrips(chunkdim(sink), sink_grid)
if (ok) sink else NULL
}
### Returns a RealizationSink + its associated grid in a named list if we
### can take the "shared sink" route, or NULL if we can't. Note that we MUST
### ALWAYS take the "shared sink" route if 'nrow(input_grid)' is 1.
make_shared_sink_and_grid_along_hstrips <-
function(BPPARAM, input_grid, sink_ncol,
BACKEND, sink_rownames, sink_colnames, ...)
{
## Note that, at the moment, we don't try the "shared sink" route if
## parallel processing is enabled because there's no guarantee that the
## realization sink will support concurrent writes (e.g. HDF5 does not).
## TODO (maybe):
## - For registered realization backends, we could register
## their ability to do concurrent writes, and decide based on that.
## - Alternatively, we could introduce a new generic (e.g.
## supports_concurrent_writing() or concurrent_writes(), to define
## in RealizationSink-class.R) with a method defined for RealizationSink
## objects that returns FALSE. Then concrete subclasses that support
## concurrent writes (e.g. TileDBRealizationSink?) would overwrite it
## with a method that returns TRUE.
if (nrow(input_grid) != 1L &&
!is.null(BPPARAM) && BiocParallel::bpnworkers(BPPARAM) >= 2L)
return(NULL)
sink_grid <- .make_sink_grid_of_hstrips(input_grid, sink_ncol)
sink <- .make_shared_sink_along_hstrips(input_grid, sink_grid, BACKEND,
sink_rownames, sink_colnames, ...)
if (is.null(sink))
return(NULL)
list(sink=sink, sink_grid=sink_grid)
}
### Returns a RealizationSink + its associated grid in a named list if we
### can take the "shared sink" route, or NULL if we can't. Note that we MUST
### ALWAYS take the "shared sink" route if 'ncol(input_grid)' is 1.
make_shared_sink_and_grid_along_vstrips <-
function(BPPARAM, input_grid, sink_nrow,
BACKEND, sink_rownames, sink_colnames, ...)
{
if (ncol(input_grid) != 1L &&
!is.null(BPPARAM) && BiocParallel::bpnworkers(BPPARAM) >= 2L)
return(NULL)
sink_grid <- .make_sink_grid_of_vstrips(input_grid, sink_nrow)
sink <- .make_shared_sink_along_vstrips(input_grid, sink_grid, BACKEND,
sink_rownames, sink_colnames, ...)
if (is.null(sink))
return(NULL)
list(sink=sink, sink_grid=sink_grid)
}
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### BLOCK_rowsum() and BLOCK_colsum()
###
### x: a matrix-like object (typically a DelayedMatrix).
### grid: an array grid (ArrayGrid object) defined on 'x'.
### Walks on the matrix blocks defined by 'grid'.
### If 'BACKEND' is NULL, returns an ordinary matrix. Otherwise, returns
### a DelayedMatrix object that is either pristine or the result of cbind'ing
### several pristine DelayedMatrix objects together (delayed cbind()).
### Calling nseed() on the returned object will return 1 in the pristine case
### or the number of objects bound together in the non-pristine case. In the
### pristine case, arguments specified thru the ellipsis will be passed to the
### RealizationSink constructor associated with 'BACKEND'. Note that the first
### 3 arguments of **any** RealizationSink constructor are guaranteed to
### be 'dim', 'dimnames', and 'type', and the arguments specified thru the
### ellipsis here can not be any of these. 'as.sparse' is not allowed either.
BLOCK_rowsum <- function(x, group, reorder=TRUE, na.rm=FALSE,
grid=NULL, as.sparse=NA,
BPPARAM=getAutoBPPARAM(), verbose=NA,
BACKEND=getAutoRealizationBackend(), ...,
dry.run=FALSE)
{
stopifnot(length(dim(x)) == 2L) # matrix-like object
verbose <- normarg_verbose(verbose)
ugroup <- as.character(S4Arrays:::compute_ugroup(group, nrow(x), reorder))
if (!isTRUEorFALSE(na.rm))
stop(wmsg("'na.rm' must be TRUE or FALSE"))
if (!isTRUEorFALSE(dry.run))
stop(wmsg("'dry.run' must be TRUE or FALSE"))
ans_dim <- c(length(ugroup), ncol(x))
## --- define INIT() ---
## INIT() must return a matrix of type "double" rather than "integer".
## This is to avoid integer overflows during the within-strip walks.
INIT <- function(j, grid, ugroup, x_colnames) {
vp <- grid[[1L, j]]
dn <- list(ugroup, extractROWS(x_colnames, ranges(vp)[2L]))
matrix(0.0, nrow=length(ugroup), ncol=ncol(vp), dimnames=dn)
}
INIT_MoreArgs <- list(ugroup=ugroup, x_colnames=colnames(x))
## --- define FINAL() ---
if (is.null(BACKEND)) {
if (dry.run)
return(list(class="matrix", dim=ans_dim, type="double"))
FINAL <- if (verbose) final_vstrip_noop else NULL
FINAL_MoreArgs <- list()
} else {
## The "shared sink" route consists in using a single realization sink
## shared across all strips. Can we take this route?
## make_shared_sink_and_grid_along_vstrips() will figure it out and
## return a RealizationSink + its associated grid in a named list if
## it turns out that we can take the "shared sink" route, or NULL if
## we can't.
grid <- best_grid_for_vstrip_apply(x, grid)
sink_and_grid <- make_shared_sink_and_grid_along_vstrips(BPPARAM,
grid, ans_dim[[1L]],
BACKEND, ugroup, colnames(x), ...)
if (is.null(sink_and_grid)) {
if (dry.run)
return(list(class="DelayedMatrix", dim=ans_dim, type="double",
nseed=ncol(grid)))
FINAL <- function(init, j, grid, BACKEND, verbose) {
realize_matrix(init, BACKEND, verbose)
}
FINAL_MoreArgs <- list(BACKEND=BACKEND, verbose=verbose)
} else {
## "shared sink" route.
if (dry.run)
return(list(class=BACKEND, dim=ans_dim, type="double",
nseed=1L))
FINAL <- function(init, j, grid, sink, sink_grid, verbose) {
write_full_sink_cols(sink, sink_grid, j, init, verbose)
}
FINAL_MoreArgs <- c(sink_and_grid, list(verbose=verbose))
}
}
## --- define FUN() ---
FUN <- function(init, block, group, ugroup, na.rm=FALSE) {
## 'block' is either an ordinary matrix or SVT_SparseMatrix object.
vp <- currentViewport()
group2 <- extractROWS(group, ranges(vp)[1L])
block_ans <- rowsum(block, group2, reorder=FALSE, na.rm=na.rm)
if (!is.matrix(block_ans))
block_ans <- as.matrix(block_ans)
m <- match(rownames(block_ans), ugroup)
init[m, ] <- init[m, ] + block_ans
init
}
FUN_MoreArgs <- list(group=group, ugroup=ugroup, na.rm=na.rm)
## --- block processing ---
strip_results <- vstrip_apply(x, INIT, INIT_MoreArgs,
FUN, FUN_MoreArgs,
FINAL, FINAL_MoreArgs,
grid=grid, as.sparse=as.sparse,
BPPARAM=BPPARAM, verbose=verbose)
## --- turn output of block processing into object and return it ---
if (is.null(BACKEND) || is.null(sink_and_grid)) {
combine_strip_results("cbind", strip_results, verbose)
} else {
## "shared sink" route.
shared_sink_as_DelayedArray(sink_and_grid$sink, verbose)
}
}
### x: a matrix-like object (typically a DelayedMatrix).
### grid: an array grid (ArrayGrid object) defined on 'x'.
### Walks on the matrix blocks defined by 'grid'.
### If 'BACKEND' is NULL, returns an ordinary matrix. Otherwise, returns
### a DelayedMatrix object that is either pristine or the result of rbind'ing
### several pristine DelayedMatrix objects together (delayed rbind()).
### See BLOCK_rowsum() above for what arguments can be specified thru the
### ellipsis.
BLOCK_colsum <- function(x, group, reorder=TRUE, na.rm=FALSE,
grid=NULL, as.sparse=NA,
BPPARAM=getAutoBPPARAM(), verbose=NA,
BACKEND=getAutoRealizationBackend(), ...,
dry.run=FALSE)
{
stopifnot(length(dim(x)) == 2L) # matrix-like object
verbose <- normarg_verbose(verbose)
ugroup <- as.character(S4Arrays:::compute_ugroup(group, ncol(x), reorder))
if (!isTRUEorFALSE(na.rm))
stop(wmsg("'na.rm' must be TRUE or FALSE"))
if (!isTRUEorFALSE(dry.run))
stop(wmsg("'dry.run' must be TRUE or FALSE"))
ans_dim <- c(nrow(x), length(ugroup))
## --- define INIT() ---
## INIT() must return a matrix of type "double" rather than "integer".
## This is to avoid integer overflows during the within-strip walks.
INIT <- function(i, grid, ugroup, x_rownames) {
vp <- grid[[i, 1L]]
dn <- list(extractROWS(x_rownames, ranges(vp)[1L]), ugroup)
matrix(0.0, nrow=nrow(vp), ncol=length(ugroup), dimnames=dn)
}
INIT_MoreArgs <- list(ugroup=ugroup, x_rownames=rownames(x))
## --- define FINAL() ---
if (is.null(BACKEND)) {
if (dry.run)
return(list(class="matrix", dim=ans_dim, type="double"))
FINAL <- if (verbose) final_hstrip_noop else NULL
FINAL_MoreArgs <- list()
} else {
## The "shared sink" route consists in using a single realization sink
## shared across all strips. Can we take this route?
## make_shared_sink_and_grid_along_hstrips() will figure it out and
## return a RealizationSink + its associated grid in a named list if
## it turns out that we can take the "shared sink" route, or NULL if
## we can't.
grid <- best_grid_for_hstrip_apply(x, grid)
sink_and_grid <- make_shared_sink_and_grid_along_hstrips(BPPARAM,
grid, ans_dim[[2L]],
BACKEND, rownames(x), ugroup, ...)
if (is.null(sink_and_grid)) {
if (dry.run)
return(list(class="DelayedMatrix", dim=ans_dim, type="double",
nseed=nrow(grid)))
FINAL <- function(init, i, grid, BACKEND, verbose) {
realize_matrix(init, BACKEND, verbose)
}
FINAL_MoreArgs <- list(BACKEND=BACKEND, verbose=verbose)
} else {
## "shared sink" route.
if (dry.run)
return(list(class=BACKEND, dim=ans_dim, type="double",
nseed=1L))
FINAL <- function(init, i, grid, sink, sink_grid, verbose) {
write_full_sink_rows(sink, sink_grid, i, init, verbose)
}
FINAL_MoreArgs <- c(sink_and_grid, list(verbose=verbose))
}
}
## --- define FUN() ---
FUN <- function(init, block, group, ugroup, na.rm=FALSE) {
## 'block' is either an ordinary matrix or SVT_SparseMatrix object.
vp <- currentViewport()
group2 <- extractROWS(group, ranges(vp)[2L])
block_ans <- colsum(block, group2, reorder=FALSE, na.rm=na.rm)
if (!is.matrix(block_ans))
block_ans <- as.matrix(block_ans)
m <- match(colnames(block_ans), ugroup)
init[ , m] <- init[ , m] + block_ans
init
}
FUN_MoreArgs <- list(group=group, ugroup=ugroup, na.rm=na.rm)
## --- block processing ---
strip_results <- hstrip_apply(x, INIT, INIT_MoreArgs,
FUN, FUN_MoreArgs,
FINAL, FINAL_MoreArgs,
grid=grid, as.sparse=as.sparse,
BPPARAM=BPPARAM, verbose=verbose)
## --- turn output of block processing into object and return it ---
if (is.null(BACKEND) || is.null(sink_and_grid)) {
combine_strip_results("rbind", strip_results, verbose)
} else {
## "shared sink" route.
shared_sink_as_DelayedArray(sink_and_grid$sink, verbose)
}
}
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### rowsum(), describe_rowsum_result(),
### colsum(), describe_colsum_result() methods
###
### S3/S4 combo for rowsum.DelayedMatrix
rowsum.DelayedMatrix <- function(x, group, reorder=TRUE, ...)
BLOCK_rowsum(x, group, reorder, ...)
setMethod("rowsum", "DelayedMatrix",
function(x, group, reorder=TRUE, na.rm=FALSE)
BLOCK_rowsum(x, group, reorder, na.rm)
)
### describe_rowsum_result().
setGeneric("describe_rowsum_result", signature="x",
function(x, group, reorder=TRUE, na.rm=FALSE)
standardGeneric("describe_rowsum_result")
)
setMethod("describe_rowsum_result", "ANY",
function(x, group, reorder=TRUE, na.rm=FALSE) NULL
)
setMethod("describe_rowsum_result", "DelayedMatrix",
function(x, group, reorder=TRUE, na.rm=FALSE)
BLOCK_rowsum(x, group, reorder, na.rm, dry.run=TRUE)
)
### colsum() method.
setMethod("colsum", "DelayedMatrix", BLOCK_colsum)
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