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new_DelayedSubset <- DelayedArray:::new_DelayedSubset
.TEST_MATRIX2a <- matrix(c(5:-2, rep.int(c(0L, 99L), 11)), ncol=6,
dimnames=list(NULL, LETTERS[1:6]))
.TEST_SVT3 <- SVT_SparseArray(dim=c(40, 100, 1))
.TEST_SVT3[Lindex2Mindex(1:50, c(10, 5, 1))] <- 1:50
.TEST_ARRAY3 <- as.array(.TEST_SVT3)
.basic_checks_on_DelayedOp_with_DIM2 <- function(a, x)
{
## We use suppressWarnings() to suppress the warnings that some
## calls to extract_array() could generate on some particular
## DelayedOp objects. For example on a DelayedUnaryIsoOpStack object
## with the log() function in its OPS stack and negative array elements
## in its seed. These warnings are expected but annoying in the context
## of unit tests.
checkIdentical(dim(a), dim(x))
checkIdentical(dimnames(a), dimnames(x))
checkIdentical(a, suppressWarnings(as.array(x)))
i2 <- c(1:2, 6:2, 2:1)
current <- suppressWarnings(extract_array(x, list(5:2, i2)))
checkIdentical(unname(a[5:2, i2]), unname(current))
current <- suppressWarnings(extract_array(x, list(5:2, NULL)))
checkIdentical(unname(a[5:2, ]), unname(current))
current <- suppressWarnings(extract_array(x, list(5:2, 2L)))
checkIdentical(unname(a[5:2, 2L, drop=FALSE]), unname(current))
current <- suppressWarnings(extract_array(x, list(5:2, integer(0))))
checkIdentical(unname(a[5:2, integer(0)]), unname(current))
}
.basic_checks_on_DelayedOp_with_DIM3 <- function(a, x)
{
checkIdentical(dim(a), dim(x))
checkIdentical(dimnames(a), dimnames(x))
checkIdentical(a, as.array(x))
i3 <- c(3:8, 1L)
current <- extract_array(x, list(i3, 6:5, NULL))
checkIdentical(unname(a[i3, 6:5, , drop=FALSE]), unname(current))
current <- extract_array(x, list(i3, c(6:5, 6L), NULL))
checkIdentical(unname(a[i3, c(6:5, 6L), , drop=FALSE]), unname(current))
current <- extract_array(x, list(i3, c(6:5, 6L), integer(0)))
checkIdentical(unname(a[i3, c(6:5, 6L), integer(0)]), unname(current))
}
.check_extract_sparse_array_on_DelayedOp_with_DIM3 <- function(a, x)
{
checkTrue(is_sparse(x))
## The behavior of extract_sparse_array() is **undefined** when the
## subscripts in 'index' contain duplicates. See "extract_sparse_array()
## contract" in SparseArray/R/extract_sparse_array.R (SparseArray package).
## So do NOT use such subscripts in the tests below.
current <- extract_sparse_array(x, list(NULL, NULL, NULL))
checkTrue(is(current, "SVT_SparseArray"))
checkIdentical(a, as.array(current))
i3 <- c(3:8, 1L)
current <- extract_sparse_array(x, list(i3, 6:5, NULL))
checkTrue(is(current, "SVT_SparseArray"))
target <- extract_array(a, list(i3, 6:5, NULL))
checkIdentical(target, as.array(current))
current <- extract_sparse_array(x, list(i3, 6:5, integer(0)))
checkTrue(is(current, "SVT_SparseArray"))
target <- extract_array(a, list(i3, 6:5, integer(0)))
checkIdentical(target, as.array(current))
}
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### test_* functions
###
test_DelayedSubset_constructor <- function(silent=FALSE)
{
## We also test nseed(), seed(), and is_noop()
x <- new_DelayedSubset()
checkTrue(is(x, "DelayedSubset"))
checkTrue(validObject(x))
checkIdentical(1L, nseed(x))
checkIdentical(new("array"), seed(x))
checkIdentical(list(NULL), x@index)
checkTrue(is_noop(x))
x <- new_DelayedSubset(.TEST_MATRIX2a)
checkTrue(is(x, "DelayedSubset"))
checkTrue(validObject(x))
checkIdentical(1L, nseed(x))
checkIdentical(.TEST_MATRIX2a, seed(x))
checkIdentical(list(NULL, NULL), x@index)
checkTrue(is_noop(x))
x <- new_DelayedSubset(.TEST_MATRIX2a, list(NULL, 5:4))
checkTrue(is(x, "DelayedSubset"))
checkTrue(validObject(x))
checkIdentical(1L, nseed(x))
checkIdentical(.TEST_MATRIX2a, seed(x))
checkIdentical(list(NULL, 5:4), x@index)
checkIdentical(FALSE, is_noop(x))
## Test normalization of user-supplied 'Nindex' argument
checkException(new_DelayedSubset(.TEST_MATRIX2a, 5:4),
silent=silent)
checkException(new_DelayedSubset(.TEST_MATRIX2a, list(5:4)),
silent=silent)
checkException(new_DelayedSubset(.TEST_MATRIX2a, list(NULL, 7:4)),
silent=silent)
checkException(new_DelayedSubset(.TEST_MATRIX2a, list(NULL, "zz")),
silent=silent)
x <- new_DelayedSubset(.TEST_MATRIX2a, list(0, c(5:4, 5.99, 6.99)))
checkTrue(is(x, "DelayedSubset"))
checkTrue(validObject(x))
checkIdentical(1L, nseed(x))
checkIdentical(.TEST_MATRIX2a, seed(x))
checkIdentical(list(integer(0), c(5:4, 5:6)), x@index)
checkIdentical(FALSE, is_noop(x))
x <- new_DelayedSubset(.TEST_MATRIX2a, list(NULL, -3))
checkTrue(is(x, "DelayedSubset"))
checkTrue(validObject(x))
checkIdentical(1L, nseed(x))
checkIdentical(.TEST_MATRIX2a, seed(x))
checkIdentical(list(NULL, c(1:2, 4:6)), x@index)
checkIdentical(FALSE, is_noop(x))
x <- new_DelayedSubset(.TEST_MATRIX2a, list(NULL, 1:6))
checkTrue(is(x, "DelayedSubset"))
checkTrue(validObject(x))
checkIdentical(1L, nseed(x))
checkIdentical(.TEST_MATRIX2a, seed(x))
checkIdentical(list(NULL, NULL), x@index)
checkTrue(is_noop(x))
x <- new_DelayedSubset(.TEST_MATRIX2a, list(-22, TRUE))
checkTrue(is(x, "DelayedSubset"))
checkTrue(validObject(x))
checkIdentical(1L, nseed(x))
checkIdentical(.TEST_MATRIX2a, seed(x))
checkIdentical(list(NULL, NULL), x@index)
checkTrue(is_noop(x))
x <- new_DelayedSubset(.TEST_MATRIX2a, list(NULL, c("E", "B", "C", "C")))
checkTrue(is(x, "DelayedSubset"))
checkTrue(validObject(x))
checkIdentical(1L, nseed(x))
checkIdentical(.TEST_MATRIX2a, seed(x))
checkIdentical(list(NULL, c(5L, 2L, 3L, 3L)), x@index)
checkIdentical(FALSE, is_noop(x))
x <- new_DelayedSubset(.TEST_MATRIX2a, list(IRanges(3:2, 5), IRanges(1, 6)))
checkTrue(is(x, "DelayedSubset"))
checkTrue(validObject(x))
checkIdentical(1L, nseed(x))
checkIdentical(.TEST_MATRIX2a, seed(x))
checkIdentical(list(c(3:5, 2:5), NULL), x@index)
checkIdentical(FALSE, is_noop(x))
checkException(new_DelayedSubset(.TEST_MATRIX2a, list(NULL, IRanges(0, 3))),
silent=silent)
checkException(new_DelayedSubset(.TEST_MATRIX2a, list(NULL, IRanges(2, 7))),
silent=silent)
}
test_DelayedSubset_API <- function()
{
## 1. Ordinary array seed -- no-op
x1 <- new_DelayedSubset(.TEST_MATRIX2a)
.basic_checks_on_DelayedOp_with_DIM2(.TEST_MATRIX2a, x1)
checkIdentical(FALSE, is_sparse(x1))
## 2. Ordinary array seed
Nindex2 <- list(5:2, c(1:2, 5, 2:1))
x2 <- new_DelayedSubset(.TEST_MATRIX2a, Nindex2)
a2 <- .TEST_MATRIX2a[5:2, c(1:2, 5L, 2:1)]
checkIdentical(dim(a2), dim(x2))
checkIdentical(dimnames(a2), dimnames(x2))
checkIdentical(a2, as.array(x2))
current <- extract_array(x2, list(NULL, 4:2))
checkIdentical(unname(a2[ , 4:2]), unname(current))
current <- extract_array(x2, list(NULL, 4L))
checkIdentical(unname(a2[ , 4L, drop=FALSE]), unname(current))
current <- extract_array(x2, list(integer(0), NULL))
checkIdentical(unname(a2[integer(0), ]), unname(current))
checkIdentical(FALSE, is_sparse(x2))
## 3. Sparse seed -- no-op
x3 <- new_DelayedSubset(.TEST_SVT3)
.basic_checks_on_DelayedOp_with_DIM3(.TEST_ARRAY3, x3)
.check_extract_sparse_array_on_DelayedOp_with_DIM3(.TEST_ARRAY3, x3)
## 4. Sparse seed -- structural sparsity propagated
i3 <- c(3:8, 1L)
index4 <- list(i3, 6:5, NULL)
x4 <- new_DelayedSubset(.TEST_SVT3, index4)
a4 <- .TEST_ARRAY3[i3, 6:5, , drop=FALSE]
checkIdentical(dim(a4), dim(x4))
checkIdentical(dimnames(a4), dimnames(x4))
checkIdentical(a4, as.array(x4))
current <- extract_array(x4, list(7:5, NULL, NULL))
checkIdentical(unname(a4[7:5, , , drop=FALSE]), unname(current))
current <- extract_array(x4, list(7:5, 2L, integer(0)))
checkIdentical(unname(a4[7:5, 2L, integer(0), drop=FALSE]), unname(current))
checkTrue(is_sparse(x4))
svt4 <- extract_sparse_array(.TEST_SVT3, index4)
## The behavior of extract_sparse_array() is **undefined** when the
## subscripts in 'index' contain duplicates. See "extract_sparse_array()
## contract" in SparseArray/R/extract_sparse_array.R (SparseArray package).
## So do NOT use such subscripts in the tests below.
current <- extract_sparse_array(x4, list(NULL, NULL, NULL))
checkTrue(is(current, "SVT_SparseArray"))
checkIdentical(svt4, current)
current <- extract_sparse_array(x4, list(c(6:7, 3:2), NULL, NULL))
target <- extract_sparse_array(svt4, list(c(6:7, 3:2), NULL, NULL))
checkIdentical(target, current)
current <- extract_sparse_array(x4, list(c(6:7, 3:2), NULL, integer(0)))
target <- extract_sparse_array(svt4, list(c(6:7, 3:2), NULL, integer(0)))
checkIdentical(target, current)
current <- extract_sparse_array(x4, list(c(6:7, 3:2), 2L, NULL))
target <- extract_sparse_array(svt4, list(c(6:7, 3:2), 2L, NULL))
checkIdentical(target, current)
## 5. Sparse seed but structural sparsity NOT propagated because
## subscripts in 'Nindex' argument contain duplicates
i3 <- c(3:8, 1L)
Nindex5 <- list(i3, c(6:5, 6L), NULL) # Nindex5[[2]] contains duplicates!
x5 <- new_DelayedSubset(.TEST_SVT3, Nindex5)
a5 <- .TEST_ARRAY3[i3, c(6:5, 6L), , drop=FALSE]
checkIdentical(dim(a5), dim(x5))
checkIdentical(dimnames(a5), dimnames(x5))
checkIdentical(a5, as.array(x5))
checkIdentical(FALSE, is_sparse(x5)) # structural sparsity not propagated!
}
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