tests/testthat/test_H5S.R

In rhdf5: R Interface to HDF5

library(rhdf5)

############################################################
context("H5Screate")
############################################################

test_that("Dataspace creation & closure", {
    expect_silent(sid <- H5Screate())
    expect_is(sid , "H5IdComponent")
    expect_silent(H5Sclose(sid))
    
    expect_silent(sid <- H5Screate(type = "H5S_SIMPLE"))
    expect_is(sid , "H5IdComponent")
    expect_silent(H5Sclose(sid))
    
    expect_silent(sid <- H5Screate(type = "H5S_NULL"))
    expect_is(sid , "H5IdComponent")
    expect_silent(H5Sclose(sid))
    
    expect_null( h5errorHandling(type = "suppress") )  
    expect_message( sid <- H5Screate(type = "FOO") )
    expect_false(sid)
})
 
############################################################
context("H5Scopy")
############################################################

test_that("Dataspace copying", {
    sid <- H5Screate()
    expect_silent(sid2 <- H5Scopy(sid))
    expect_false( identical(sid, sid2) )
    expect_silent(H5Sclose(sid))
    expect_silent(H5Sclose(sid2))
})

test_that("Dataspace copy fails on bad input", {
    expect_error(sid <- H5Scopy("foo"))
})

############################################################
context("H5S simple")
############################################################

test_that("We can create a simple dataspace", {
    expect_silent(sid <- H5Screate_simple(dims = c(10,2)))
    expect_is(sid , "H5IdComponent")
    expect_true(H5Sis_simple(sid))
    
    expect_is(dspace_dims <- H5Sget_simple_extent_dims(sid), "list")
    expect_named(dspace_dims, c("rank", "size", "maxsize"))
    expect_equal(dspace_dims$size, dspace_dims$maxsize)
    expect_equal(dspace_dims$rank, 2)
    
    expect_silent(H5Sset_extent_simple(sid, dims = c(1,2,3), maxdims = c(10,20,30)))
    expect_is(dspace_dims <- H5Sget_simple_extent_dims(sid), "list")
    expect_false( identical(dspace_dims$size, dspace_dims$maxsize) )
    expect_equal(dspace_dims$rank, 3)
    
    expect_silent(H5Sclose(sid))
})

############################################################
context("H5S Select Hyperslab")
############################################################

test_that("Selecting hyperslabs", {
    
    expect_silent(sid <- H5Screate_simple(dims = c(10,20)))

    expect_silent( H5Sselect_hyperslab(sid) )

    ## errors when not providing enough dimensions
    expect_error( H5Sselect_hyperslab(sid, start = 2) )
    expect_error( H5Sselect_hyperslab(sid, stride = 2) )
    expect_error( H5Sselect_hyperslab(sid, count = 2) )
    expect_error( H5Sselect_hyperslab(sid, block = 2) )
    
    expect_silent(H5Sclose(sid))
    
    ## error in incorrect input
    expect_error(  H5Sselect_hyperslab("foo") )
})

############################################################
context("H5S Select Index")
############################################################

test_that("Selecting using an index", {
    
    expect_silent(sid <- H5Screate_simple(dims = c(10,20,30)))
    
    expect_silent( size <- H5Sselect_index(sid, index = list(1:5, 1:5, 11:15)) )
    expect_identical( size, c(5,5,5) )
    
    expect_silent( size <- H5Sselect_index(sid, index = list(NULL, NULL, NULL)) )
    expect_identical( size, c(10,20,30) )
    
    ## errors when not providing enough dimensions or incorrect dimensions
    expect_error( H5Sselect_index(sid, index = list(10)),
                  regexp = "length of list index not equal to h5space dimensional extension")
    expect_error( H5Sselect_index(sid, index = list(1:5, 1:5, 0:5)), 
                  regexp = "negative indices and 0 not supported" )
    expect_error( H5Sselect_index(sid, index = list(1:15, 1:5, 1:5)), 
                  regexp = "index exceeds HDF5-array dimension")
    
    expect_silent(H5Sclose(sid))
})

############################################################
context("H5S cleanup")
##########################################################

test_that("No open HDF5 objects are left", {
    expect_equal( length(h5validObjects()), 0 )
})