tests/testthat/test_external_filters.R

In grimbough/rhdf5: R Interface to HDF5

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
    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()