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#setAutoRealizationBackend("RleArray")
#setAutoRealizationBackend("HDF5Array")
Arith_members <- c("+", "-", "*", "/", "^", "%%", "%/%")
Compare_members <- c("==", "!=", "<=", ">=", "<", ">")
Logic_members <- c("&", "|") # currently untested
a1 <- array(sample(5L, 150, replace=TRUE), c(5, 10, 3)) # integer array
a2 <- a1 + runif(150) - 0.5 # numeric array
m2 <- matrix(runif(60), ncol=6) # numeric matrix
block_sizes1 <- c(12L, 20L, 50L, 15000L)
block_sizes2 <- 2L * block_sizes1
test_DelayedMatrix_Ops <- function()
{
test_delayed_Ops_on_matrix <- function(.Generic, m, M) {
GENERIC <- match.fun(.Generic)
target_current <- list(
list(GENERIC(m, m[ , 1]), GENERIC(M, M[ , 1])),
list(GENERIC(m[ , 2], m), GENERIC(M[ , 2], M))
)
for (i in seq_along(target_current)) {
target <- target_current[[i]][[1L]]
current <- target_current[[i]][[2L]]
checkIdentical(target, as.matrix(current))
checkIdentical(t(target), as.matrix(t(current)))
checkIdentical(target[-2, 8:5], as.matrix(current[-2, 8:5]))
checkIdentical(t(target[-2, 8:5]), as.matrix(t(current[-2, 8:5])))
checkIdentical(target[-2, 0], as.matrix(current[-2, 0]))
checkIdentical(t(target[-2, 0]), as.matrix(t(current[-2, 0])))
checkIdentical(target[0, ], as.matrix(current[0, ]))
checkIdentical(t(target[0, ]), as.matrix(t(current[0, ])))
}
target_current <- list(
list(GENERIC(t(m), 8:-1), GENERIC(t(M), 8:-1)),
list(GENERIC(8:-1, t(m)), GENERIC(8:-1, t(M))),
list(GENERIC(t(m), m[1 , ]), GENERIC(t(M), M[1 , ])),
list(GENERIC(m[2 , ], t(m)), GENERIC(M[2 , ], t(M))),
list(GENERIC(t(m), m[1 , 6:10]), GENERIC(t(M), M[1 , 6:10])),
list(GENERIC(m[2 , 8:7], t(m)), GENERIC(M[2 , 8:7], t(M)))
)
for (i in seq_along(target_current)) {
target <- target_current[[i]][[1L]]
current <- target_current[[i]][[2L]]
checkIdentical(target, as.matrix(current))
checkIdentical(target[1:3 , ], as.matrix(current[1:3 , ]))
checkIdentical(target[ , 1:3], as.matrix(current[ , 1:3]))
checkIdentical(t(target), as.matrix(t(current)))
checkIdentical(t(target)[1:3 , ], as.matrix(t(current)[1:3 , ]))
checkIdentical(t(target)[ , 1:3], as.matrix(t(current)[ , 1:3]))
checkIdentical(target[8:5, -2], as.matrix(current[8:5, -2]))
checkIdentical(t(target[8:5, -2]), as.matrix(t(current[8:5, -2])))
checkIdentical(target[0, -2], as.matrix(current[0, -2]))
checkIdentical(t(target[0, -2]), as.matrix(t(current[0, -2])))
checkIdentical(target[ , 0], as.matrix(current[ , 0]))
checkIdentical(t(target[ , 0]), as.matrix(t(current[ , 0])))
}
}
a <- a2
a[2, 9, 2] <- NA # same as a[[92]] <- NA
toto <- function(x) t((5 * x[ , 1:2] ^ 3 + 1L) * log(x)[, 10:9])[ , -1]
m <- a[ , , 2]
M <- realize(m)
checkIdentical(toto(m), as.array(toto(M)))
## "Logic" members currently untested.
for (.Generic in c(Arith_members, Compare_members))
test_delayed_Ops_on_matrix(.Generic, m, M)
M <- realize(a)[ , , 2]
checkIdentical(toto(m), as.array(toto(M)))
for (.Generic in c(Arith_members, Compare_members))
test_delayed_Ops_on_matrix(.Generic, m, M)
}
test_DelayedMatrix_mult <- function()
{
m <- m2
m[2, 4] <- NA
m[5, 4] <- Inf
m[6, 3] <- -Inf
M <- realize(m)
# These two need to be smaller than 'M' to test both schemes.
Lm <- rbind(rep(1L, 10), rep(c(1L, 0L), 5), rep(-100L, 10))
Rm <- rbind(Lm + 7.05, 0.1 * Lm)[,1:5]
on.exit(suppressMessages(setAutoBlockSize()))
for (block_size in block_sizes2) {
suppressMessages(setAutoBlockSize(block_size))
P <- Lm %*% M
checkEquals(Lm %*% m, as.matrix(P))
P <- M %*% Rm
checkEquals(m %*% Rm, as.matrix(P))
P <- crossprod(t(Lm), M)
checkEquals(crossprod(t(Lm), m), as.matrix(P))
P <- tcrossprod(M, t(Rm))
checkEquals(tcrossprod(m, t(Rm)), as.matrix(P))
}
# Handles sparse inputs.
s <- Matrix::rsparsematrix(nrow(m2), ncol(m2), density=0.2)
S <- DelayedArray(s)
for (block_size in block_sizes2) {
suppressMessages(setAutoBlockSize(block_size))
P <- Lm %*% S
checkEquals(unname(as.matrix(Lm %*% s)), as.matrix(P))
P <- S %*% Rm
checkEquals(unname(as.matrix(s %*% Rm)), as.matrix(P))
P <- crossprod(t(Lm), S)
checkEquals(unname(as.matrix(crossprod(t(Lm), s))), as.matrix(P))
P <- tcrossprod(S, t(Rm))
checkEquals(unname(as.matrix(tcrossprod(s, t(Rm)))), as.matrix(P))
}
# Handles two DelayedMatrices being multiplied togehter.
y1 <- matrix(runif(100), ncol=5)
y2 <- matrix(runif(100), nrow=5)
Y1 <- DelayedArray(y1)
Y2 <- DelayedArray(y2)
ref <- y1 %*% y2
for (block_size in block_sizes2) {
suppressMessages(setAutoBlockSize(block_size))
out <- Y1 %*% Y2
checkEquals(ref, as.matrix(out))
out <- crossprod(t(Y1), Y2)
checkEquals(ref, as.matrix(out))
out <- tcrossprod(Y1, t(Y2))
checkEquals(ref, as.matrix(out))
}
# Throws errors correctly.
checkException(Lm[,1,drop=FALSE] %*% m, msg="non-conformable")
}
test_DelayedMatrix_crossprod_self <- function()
{
M <- DelayedArray(m2)
# Checking self-product in a core-agnostic way.
on.exit(suppressMessages(setAutoBlockSize()))
for (block_size in block_sizes2) {
suppressMessages(setAutoBlockSize(block_size))
checkEquals(as.matrix(crossprod(M)), crossprod(m2))
checkEquals(as.matrix(tcrossprod(M)), tcrossprod(m2))
}
# Checking self-product in a non-core-agnostic way.
DelayedArray:::setAutoMultParallelAgnostic(FALSE)
on.exit(DelayedArray:::setAutoMultParallelAgnostic())
for (block_size in block_sizes2) {
suppressMessages(setAutoBlockSize(block_size))
checkEquals(as.matrix(crossprod(M)), crossprod(m2))
checkEquals(as.matrix(tcrossprod(M)), tcrossprod(m2))
}
}
test_DelayedMatrix_mult_parallel <- function()
{
setAutoBPPARAM(BiocParallel::SnowParam(2))
on.exit(setAutoBPPARAM())
suppressMessages(setAutoBlockSize(10000))
on.exit(suppressMessages(setAutoBlockSize()), add=TRUE)
M <- DelayedArray(m2)
Lm <- matrix(runif(20), ncol=10)
Rm <- matrix(runif(12), nrow=6)
P <- Lm %*% M
checkEquals(Lm %*% m2, as.matrix(P))
P <- M %*% Rm
checkEquals(m2 %*% Rm, as.matrix(P))
checkEquals(as.matrix(crossprod(M)), crossprod(m2))
checkEquals(as.matrix(tcrossprod(M)), tcrossprod(m2))
DelayedArray:::setAutoMultParallelAgnostic(FALSE)
on.exit(DelayedArray:::setAutoMultParallelAgnostic(), add=TRUE)
checkEquals(as.matrix(crossprod(M)), crossprod(m2))
checkEquals(as.matrix(tcrossprod(M)), tcrossprod(m2))
}
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