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## Test image slicing operators. They need to conform to rules that are slightly
## different to those for R matrices.
##
## These rules are: spacing needs to be uniform per dimension
## i.e. im[c(1,2,11),] is not accepted
## This means that creating reflected images isn't possible
## with slicing - use slicing + Tile.
## Dropping dimensions is the default, but SimpleITK does not
## support 1D images. The slicing operator will issue a warning if
## this is attempted.
##
## The bracket operator used for slicing now constructs calls to Slice and Extract,
## rather than using special C routines. This means that the operation is multithreaded
## and preserves spacing, origin and direction.
library(SimpleITK)
slicingOperatorUnitSpacingTest<- function()
{
## Cropping test - unit spacing
im <- Image(15,15,"sitkFloat64")
im$SetSpacing(c(0.3,0.6))
t <- 0.4
ct <- cos(t)
st <- sin(t)
im$SetDirection(c(ct,-st,st,ct))
e1 <- im[2:10,3:5]
ef <- ExtractImageFilter()
ef$SetSize(c(9,3))
ef$SetIndex(c(1,2))
e2 <- ef$Execute(im)
## meta-data for slicing operator should match the metadata for the extract
## filter which we know to be correct.
if(!all(e1$GetOrigin() == e2$GetOrigin()))
{
cat("slicing operator failed, origins don't match")
quit(save="no", status=1)
}
if(!all(e1$GetSpacing() == e2$GetSpacing()))
{
cat("slicing operator failed, spacings don't match")
quit(save="no", status=1)
}
if(!all(e1$GetDirection() == e2$GetDirection()))
{
cat("slicing operator failed, directions don't match")
quit(save="no", status=1)
}
}
dirToMat <- function(im)
{
## produce an R formatted direction matrix
d1 <- im$GetDirection()
dim(d1) <- c(2,2)
d1 <- t(d1)
return(d1)
}
slicingOperatorNegativeSpacingTest<- function()
{
## Cropping test - unit spacing
im <- Image(15,15,"sitkFloat64")
im$SetSpacing(c(0.3,0.6))
t <- 0.4
ct <- cos(t)
st <- sin(t)
im$SetDirection(c(ct,-st,st,ct))
e1 <- im[2:10,5:3]
## meta-data for slicing operator should match the metadata for the extract
## filter which we know to be correct.
if(!all(e1$GetOrigin() == im$TransformIndexToPhysicalPoint(c(1,4))))
{
cat("slicing operator failed, origins don't match")
quit(save="no", status=1)
}
d1 <- dirToMat(im)
d2 <- dirToMat(e1)
## reversed the second dimension, so d2[,2] == -d1[,2]
## negate the second column and compare to original
d2[,2] <- -d2[,2]
if(!all(d1 == d2))
{
cat("slicing operator failed, directions incorrect")
quit(save="no", status=1)
}
}
slicingPositionChecks <- function()
{
x<-rep(1:10, rep(12, 10))
dim(x) <- c(12, 10)
x[5:9, 6:9] <- 21
xim <- as.image(x)
row3 <- as.array(xim[,3,drop=FALSE])
if (!(all(row3 == 3))) {
cat("Incorrect pixel values - should be all 3\n")
quit(save="no", status=1)
}
b <- as.array(xim[5:9, 6:9])
if (!all(b==21)) {
cat("Failed block extract - voxels should have value 21\n")
quit(save="no", status=1)
}
}
slicingOperatorWarningsErrors <- function()
{
im <- Image(15,15,"sitkFloat64")
## this should issue a warning
msg <- list()
try(msg <- tools::assertWarning(im[1, 2:3]), silent=TRUE)
if (length(msg) == 0) {
cat("Slicing operator should have issued a warning, but did not.\n")
quit(save="no", status=1)
}
## Turning drop off - no warning
msg <- list()
try(msg <- tools::assertCondition(im[1, 2:3, ,drop=FALSE]), silent=TRUE)
if (length(msg) != 0) {
cat("Slicing operator issued a warning/error, but should not.\n")
quit(save="no", status=1)
}
## Irregular spacing - should issue an error
msg <- list()
try(msg <- tools::assertError(im[c(1,2, 4), 2:3]), silent=TRUE)
if (length(msg) == 0) {
cat("Slicing operator should have issued an error, but did not.\n")
quit(save="no", status=1)
}
}
slicingSyntaxTrials <- function()
{
im2 <- Image(15,15,"sitkFloat64")
im3 <- Image(15,15, 15, "sitkFloat64")
## slicing requires all dimensions to be included - these should produce an
## error
msg <- list()
try(msg <- tools::assertError(im3[1:2, 2:3]), silent=TRUE)
if (length(msg) == 0) {
cat("Slicing operator should have issued an error, but did not.\n")
quit(save="no", status=1)
}
msg <- list()
try(msg <- tools::assertError(im3[1, 2:3,drop=TRUE]), silent=TRUE)
if (length(msg) == 0) {
cat("Slicing operator should have issued an error, but did not.\n")
quit(save="no", status=1)
}
## this should be OK
msg <- list()
try(msg <- tools::assertCondition(im3[1:2, 2:3,]), silent=TRUE)
if (length(msg) != 0) {
cat("Slicing issued an error/warning, but should not.\n")
quit(save="no", status=1)
}
msg <- list()
try(msg <- tools::assertCondition(im3[1:2, 2:3,,drop=FALSE]), silent=TRUE)
if (length(msg) != 0) {
cat("Slicing issued an error/warning, but should not.\n")
quit(save="no", status=1)
}
## this should be OK
msg <- list()
try(msg <- tools::assertCondition(im3[1:2, ,2:3,]), silent=TRUE)
if (length(msg) != 0) {
cat("Slicing issued an error/warning, but should not.\n")
quit(save="no", status=1)
}
## dropping tests
j<-im3[,,3,drop=FALSE]
if (any(j$GetSize() != c(15, 15, 1))) {
cat("Image slicing error - incorrect dimensions returned\n")
cat("Expected [15, 15, 1] - got [", j$GetSize(), "]\n")
quit(save="no", status=1)
}
j<-im3[,,3,drop=TRUE]
if (any(j$GetSize() != c(15, 15))) {
cat("Image slicing error - incorrect dimensions returned\n")
cat("Expected [15, 15] - got [", j$GetSize(), "]\n")
quit(save="no", status=1)
}
## logical indexing, with variables
xidx <- (1:im3$GetWidth()) > 5
msg <- list()
try(msg <- tools::assertCondition(im3[xidx, ,2:3]), silent=TRUE)
if (length(msg) != 0) {
cat("Slicing using logical issued an error/warning, but should not.\n")
quit(save="no", status=1)
}
}
slicingZeroIndexTrials <- function()
{
## various forms of indexes are illegal because we can't support
## an "empty" image in the way R supports an "empty" array
im3 <- Image(15,15, 15, "sitkFloat64")
## error caused by calling with c()
msg <- list()
try(msg <- tools::assertError(im3[c(), 2:3,]), silent=TRUE)
if (length(msg) == 0) {
cat("Slicing operator should have issued an error, but did not.\n")
quit(save="no", status=1)
}
## check the 3rd dimension, which is handled differently to the first 2
msg <- list()
try(msg <- tools::assertError(im3[2:3, 2:3, c()]), silent=TRUE)
if (length(msg) == 0) {
cat("Slicing operator should have issued an error, but did not.\n")
quit(save="no", status=1)
}
## check 0
msg <- list()
try(msg <- tools::assertError(im3[2:3, 0, 2:3]), silent=TRUE)
if (length(msg) == 0) {
cat("Slicing operator should have issued an error, but did not.\n")
quit(save="no", status=1)
}
msg <- list()
try(msg <- tools::assertError(im3[2:3, 2:3, 0]), silent=TRUE)
if (length(msg) == 0) {
cat("Slicing operator should have issued an error, but did not.\n")
quit(save="no", status=1)
}
}
slicingOperatorUnitSpacingTest()
slicingOperatorNegativeSpacingTest()
slicingPositionChecks()
slicingSyntaxTrials()
slicingZeroIndexTrials()
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