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#setRealizationBackend("RleArray")
#setRealizationBackend("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
block_sizes1 <- c(12L, 20L, 50L, 15000L)
block_sizes2 <- 2L * block_sizes1
test_DelayedArray_unary_ops <- function()
{
a <- 2:-2 / (a1 - 3)
a[2, 9, 2] <- NA # same as a[[92]] <- NA
A <- realize(a)
for (.Generic in c("is.na", "is.finite", "is.infinite", "is.nan")) {
GENERIC <- match.fun(.Generic)
checkIdentical(GENERIC(a), as.array(GENERIC(A)))
}
a <- array(sample(c(LETTERS, letters), 60, replace=TRUE), 5:3)
A <- realize(a)
## For some obscure reason, the tests below fail in the context of
## 'DelayedArray:::.test()' or 'R CMD check'.
## TODO: Investigate this.
#for (.Generic in c("nchar", "tolower", "toupper")) {
# GENERIC <- match.fun(.Generic)
# checkIdentical(GENERIC(a), as.array(GENERIC(A)))
#}
}
test_DelayedArray_Math_ans_Arith <- function()
{
toto1 <- function(a) { 100 / floor(abs((5 * log(a + 0.2) - 1)^3)) }
toto2 <- function(a) { 100L + (5L * (a - 2L)) %% 7L }
## with an integer array
a <- a1
a[2, 9, 2] <- NA # same as a[[92]] <- NA
A <- realize(a)
## Not sure what's going on but it seems that this call to checkIdentical()
## crashes the RUnit package but only when the tests are run by
## 'R CMD check'.
#checkIdentical(toto2(a), as.array(toto2(A)))
## with a numeric array
a <- a2
a[2, 9, 2] <- NA # same as a[[92]] <- NA
A <- realize(a)
checkIdentical(toto1(a), as.array(toto1(A)))
checkIdentical(toto2(a), as.array(toto2(A)))
checkIdentical(toto2(toto1(a)), as.array(toto2(toto1(A))))
checkIdentical(toto1(toto2(a)), as.array(toto1(toto2(A))))
a <- a[ , 10:4, -2]
A <- A[ , 10:4, -2]
checkIdentical(toto1(a), as.array(toto1(A)))
checkIdentical(toto2(a), as.array(toto2(A)))
checkIdentical(toto2(toto1(a)), as.array(toto2(toto1(A))))
checkIdentical(toto1(toto2(a)), as.array(toto1(toto2(A))))
## with a numeric matrix
m <- a[ , , 2]
M <- realize(m)
checkIdentical(toto1(m), as.matrix(toto1(M)))
checkIdentical(t(toto1(m)), as.matrix(toto1(t(M))))
checkIdentical(t(toto1(m)), as.matrix(t(toto1(M))))
M <- A[ , , 2]
checkIdentical(toto1(m), as.matrix(toto1(M)))
checkIdentical(t(toto1(m)), as.matrix(toto1(t(M))))
checkIdentical(t(toto1(m)), as.matrix(t(toto1(M))))
}
test_DelayedArray_Ops_with_left_or_right_vector <- function()
{
test_delayed_Ops_on_array <- function(.Generic, a, A, m, M) {
on.exit(setAutoBlockSize())
GENERIC <- match.fun(.Generic)
target_current <- list(
list(GENERIC(a, m[ , 1]), GENERIC(A, M[ , 1])),
list(GENERIC(m[ , 1], a), GENERIC(M[ , 1], A)),
list(GENERIC(a, a[ , 1, 1]), GENERIC(A, A[ , 1, 1])),
list(GENERIC(a[ , 1, 1], a), GENERIC(A[ , 1, 1], A)),
list(GENERIC(a, a[[1]]), GENERIC(A, A[[1]])),
list(GENERIC(a[[1]], a), GENERIC(A[[1]], A))
)
for (i in seq_along(target_current)) {
target <- target_current[[i]][[1L]]
current <- target_current[[i]][[2L]]
checkIdentical(target, as.array(current))
checkIdentical(target[5:3, , -2], as.array(current[5:3, , -2]))
checkIdentical(target[0, 0, 0], as.array(current[0, 0, 0]))
checkIdentical(target[0, 0, -2], as.array(current[0, 0, -2]))
checkIdentical(target[ , 0, ], as.array(current[ , 0, ]))
for (block_size in block_sizes2) {
setAutoBlockSize(block_size)
checkEquals(sum(target, na.rm=TRUE), sum(current, na.rm=TRUE))
}
}
}
a <- a2
a[2, 9, 2] <- NA # same as a[[92]] <- NA
A <- realize(a)
m <- a[ , , 2]
M <- realize(m)
## "Logic" members currently untested.
for (.Generic in c(Arith_members, Compare_members))
test_delayed_Ops_on_array(.Generic, a, A, m, M)
## Takes too long and probably not that useful.
#M <- A[ , , 2]
#for (.Generic in c(Arith_members, Compare_members))
# test_delayed_Ops_on_array(.Generic, a, A, m, M)
}
test_DelayedArray_Ops_COMBINE_seeds <- function()
{
## comparing 2 DelayedArray objects
A1 <- realize(a1)
A2 <- realize(a2)
a3 <- array(sample(5L, 150, replace=TRUE), c(5, 10, 3))
a3[2, 9, 2] <- NA # same as a3[[92]] <- NA
A3 <- realize(a3)
## "Logic" members currently untested.
for (.Generic in c(Arith_members, Compare_members)) {
GENERIC <- match.fun(.Generic)
target1 <- GENERIC(a1, a2)
target2 <- GENERIC(a2, a1)
target3 <- GENERIC(a1, a3)
checkIdentical(target1, as.array(GENERIC(A1, A2)))
checkIdentical(target2, as.array(GENERIC(A2, A1)))
checkIdentical(target3, as.array(GENERIC(A1, A3)))
}
}
test_DelayedArray_anyNA <- function()
{
on.exit(setAutoBlockSize())
BLOCK_anyNA <- DelayedArray:::.BLOCK_anyNA
A1 <- realize(a1)
a <- a1
a[2, 9, 2] <- NA # same as a[[92]] <- NA
A <- realize(a)
for (block_size in block_sizes2) {
setAutoBlockSize(block_size)
checkIdentical(FALSE, anyNA(A1))
checkIdentical(FALSE, BLOCK_anyNA(a1))
checkIdentical(TRUE, anyNA(A))
checkIdentical(TRUE, BLOCK_anyNA(a))
}
}
test_DelayedArray_which <- function()
{
on.exit(setAutoBlockSize())
BLOCK_which <- DelayedArray:::BLOCK_which
a <- a1 == 1L
a[2, 9, 2] <- NA # same as a[[92]] <- NA
A <- realize(a)
target1 <- which(a)
target2 <- which(a, arr.ind=TRUE, useNames=FALSE)
for (block_size in block_sizes2) {
setAutoBlockSize(block_size)
checkIdentical(target1, which(A))
checkIdentical(target2, which(A, arr.ind=TRUE))
checkIdentical(target1, BLOCK_which(a))
}
a <- a1 == -1L # all FALSE
a[2, 9, 2] <- NA # same as a[[92]] <- NA
A <- realize(a)
target1 <- integer(0)
target2 <- matrix(integer(0), ncol=3)
for (block_size in block_sizes2) {
setAutoBlockSize(block_size)
checkIdentical(target1, which(A))
checkIdentical(target2, which(A, arr.ind=TRUE))
checkIdentical(target1, BLOCK_which(a))
}
}
test_DelayedArray_Summary <- function()
{
test_Summary <- function(.Generic, a, block_sizes) {
on.exit(setAutoBlockSize())
BLOCK_Summary <- DelayedArray:::.BLOCK_Summary
GENERIC <- match.fun(.Generic)
target1 <- GENERIC(a)
target2 <- GENERIC(a, na.rm=TRUE)
A <- realize(a)
for (block_size in block_sizes) {
setAutoBlockSize(block_size)
checkIdentical(target1, GENERIC(A))
checkIdentical(target1, GENERIC(aperm(A)))
checkIdentical(target1, BLOCK_Summary(.Generic, a))
checkIdentical(target2, GENERIC(A, na.rm=TRUE))
checkIdentical(target2, GENERIC(aperm(A), na.rm=TRUE))
checkIdentical(target2, BLOCK_Summary(.Generic, a, na.rm=TRUE))
}
}
## on an integer array
a <- a1
a[2, 9, 2] <- NA # same as a[[92]] <- NA
#for (.Generic in c("max", "min", "range", "sum", "prod")) {
for (.Generic in c("max", "min", "range", "sum"))
test_Summary(.Generic, a, block_sizes1)
## on a numeric array
a <- a2
a[2, 9, 2] <- NA # same as a[[92]] <- NA
a[2, 10, 2] <- Inf # same as a[[97]] <- Inf
for (.Generic in c("max", "min", "range", "sum", "prod"))
test_Summary(.Generic, a, block_sizes2)
## on a logical array
a <- array(c(rep(NA, 62), rep(TRUE, 87), FALSE), c(5, 10, 3))
for (.Generic in c("any", "all"))
test_Summary(.Generic, a, block_sizes1)
}
test_DelayedArray_mean <- function()
{
on.exit(setAutoBlockSize())
## on a numeric array
a <- a2
a[2, 9, 2] <- NA # same as a[[92]] <- NA
A <- realize(a)
target1 <- mean(a)
target2 <- mean(a, na.rm=TRUE)
target3 <- mean(a[ , 10:4, -2])
for (block_size in block_sizes2) {
setAutoBlockSize(block_size)
checkIdentical(target1, mean(A))
checkIdentical(target1, mean(aperm(A)))
checkIdentical(target2, mean(A, na.rm=TRUE))
checkIdentical(target2, mean(aperm(A), na.rm=TRUE))
checkIdentical(target3, mean(A[ , 10:4, -2]))
checkIdentical(target3, mean(aperm(A[ , 10:4, -2])))
}
}
test_DelayedArray_apply <- function()
{
test_apply <- function(a) {
A <- realize(a)
for (MARGIN in seq_along(dim(a))) {
checkIdentical(apply(a, MARGIN, dim),
apply(A, MARGIN, dim))
checkIdentical(apply(a, MARGIN, sum),
apply(A, MARGIN, sum))
checkIdentical(apply(a, MARGIN, sum, na.rm=TRUE),
apply(A, MARGIN, sum, na.rm=TRUE))
## row/colSums and row/colMeans don't work yet in that case.
if (dim(A)[[MARGIN]] == 0L && length(dim(A)) >= 3L)
next
checkIdentical(apply(a, MARGIN, rowSums),
apply(A, MARGIN, rowSums))
checkIdentical(apply(a, MARGIN, rowSums, na.rm=TRUE),
apply(A, MARGIN, rowSums, na.rm=TRUE))
checkIdentical(apply(a, MARGIN, colMeans),
apply(A, MARGIN, colMeans))
checkIdentical(apply(a, MARGIN, colMeans, na.rm=TRUE),
apply(A, MARGIN, colMeans, na.rm=TRUE))
}
}
a <- a1
a[2, 9, 2] <- NA # same as a[[92]] <- NA
test_apply(a)
test_apply(a[ , , 0])
dimnames(a) <- list(NULL, NULL, LETTERS[1:3])
test_apply(a)
test_apply(a[ , , 0])
dimnames(a) <- list(NULL, letters[1:10], LETTERS[1:3])
test_apply(a)
test_apply(a[ , , 0])
}
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