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library(rhdf5)
h5File <- tempfile(pattern = "ex_save", fileext = ".h5")
vec <- as.integer(rexp(2000, rate = 1.5))
############################################################
context("Writing Using External Filters")
############################################################
fid <- H5Fcreate(h5File)
sid <- H5Screate_simple(dims = 2000, maxdims = 2000)
tid <- rhdf5:::.setDataType(H5type = NULL, storage.mode = "integer")
test_that("BZIP2 filter works for writing", {
skip_if_not_installed('rhdf5filters')
expect_silent( dcpl <- H5Pcreate("H5P_DATASET_CREATE") )
expect_silent( H5Pset_fill_time( dcpl, "H5D_FILL_TIME_ALLOC" ) )
expect_silent( H5Pset_chunk( dcpl, 200) )
expect_silent( H5Pset_bzip2(dcpl) )
expect_silent( did <- H5Dcreate(fid, "bzip2", tid, sid, dcpl = dcpl) )
expect_silent( H5Dwrite(buf = vec, h5dataset = did) )
expect_silent( H5Dclose(did) )
})
test_that("BLOSC filter works for writing", {
skip_if_not_installed('rhdf5filters')
expect_silent( dcpl <- H5Pcreate("H5P_DATASET_CREATE") )
expect_silent( H5Pset_fill_time( dcpl, "H5D_FILL_TIME_ALLOC" ) )
expect_silent( H5Pset_chunk( dcpl, 200) )
expect_silent( H5Pset_blosc(dcpl, tid, method = 1L) )
expect_silent( did <- H5Dcreate(fid, "blosc_lz", tid, sid, dcpl = dcpl) )
expect_silent( H5Dwrite(buf = vec, h5dataset = did) )
expect_silent( H5Dclose(did) )
})
test_that("LZF filter works for writing", {
skip_if_not_installed('rhdf5filters', minimum_version = '1.3.4')
expect_silent( dcpl <- H5Pcreate("H5P_DATASET_CREATE") )
expect_silent( H5Pset_fill_time( dcpl, "H5D_FILL_TIME_ALLOC" ) )
expect_silent( H5Pset_chunk( dcpl, 200) )
expect_silent( H5Pset_lzf(dcpl, tid) )
expect_silent( did <- H5Dcreate(fid, "lzf", tid, sid, dcpl = dcpl) )
expect_silent( H5Dwrite(buf = vec, h5dataset = did) )
expect_silent( H5Dclose(did) )
})
H5Sclose(sid)
H5Fclose(fid)
############################################################
context("Reading Using External Filters")
############################################################
fid <- H5Fopen(h5File)
test_that("BZIP2 filter works when reading", {
skip_if_not_installed('rhdf5filters')
expect_silent( did <- H5Dopen(fid, name = "bzip2") )
expect_equivalent( H5Dread(did), vec)
## if compression worked the dataset should be smaller than 8000 bytes
expect_lt( H5Dget_storage_size(did), 4 * 2000 )
expect_silent( H5Dclose(did) )
})
test_that("BLOSC filter works when reading", {
skip_if_not_installed('rhdf5filters')
expect_silent( did <- H5Dopen(fid, name = "blosc_lz") )
expect_equivalent( H5Dread(did), vec)
## if compression worked the dataset should be smaller than 8000 bytes
skip(message = "FIXME: Test results in 'Error in h5checktype(). H5Identifier not valid.' which might be related to rhdf5filters")
expect_lt( H5Dget_storage_size(did), 4 * 2000 )
expect_silent( H5Dclose(did) )
})
test_that("LZF filter works when reading", {
skip_if_not_installed('rhdf5filters', minimum_version = '1.3.4')
expect_silent( did <- H5Dopen(fid, name = "lzf") )
expect_equivalent( H5Dread(did), vec)
## if compression worked the dataset should be smaller than 8000 bytes
expect_lt( H5Dget_storage_size(did), 4 * 2000 )
expect_silent( H5Dclose(did) )
})
H5Fclose(fid)
h5closeAll()
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