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Support BITSHUFFLE option of Blosc >= v0.7.3 #899

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Feb 4, 2022
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Support BITSHUFFLE option of Blosc >= v0.7.3 #899

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2 changes: 1 addition & 1 deletion filters/H5Zblosc/Project.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -8,5 +8,5 @@ HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"

[compat]
HDF5 = "0.16"
Blosc = "0.7.1"
Blosc = "0.7.3"
julia = "1.3"
13 changes: 10 additions & 3 deletions filters/H5Zblosc/src/H5Zblosc.jl
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Expand Up @@ -8,6 +8,8 @@ import HDF5.Filters: filterid, register_filter, filtername, filter_func, filter_

export H5Z_FILTER_BLOSC, blosc_filter, BloscFilter

# Import Blosc shuffle constants
import Blosc: NOSHUFFLE, SHUFFLE, BITSHUFFLE

const H5Z_FILTER_BLOSC = API.H5Z_filter_t(32001) # Filter ID registered with the HDF Group for Blosc
const FILTER_BLOSC_VERSION = 2
Expand Down Expand Up @@ -65,7 +67,7 @@ function blosc_filter(flags::Cuint, cd_nelmts::Csize_t,
# Compression level:
clevel = cd_nelmts >= 5 ? unsafe_load(cd_values, 5) : Cuint(5)
# Do shuffle:
doshuffle = cd_nelmts >= 6 ? unsafe_load(cd_values, 6) != 0 : true
doshuffle = cd_nelmts >= 6 ? unsafe_load(cd_values, 6) : SHUFFLE

if (flags & API.H5Z_FLAG_REVERSE) == 0 # compressing
# Allocate an output buffer exactly as long as the input data; if
Expand Down Expand Up @@ -134,7 +136,8 @@ struct BloscFilter <: Filter
compcode::Cuint
end

function BloscFilter(;level=5, shuffle=true, compressor="blosclz")
function BloscFilter(;level=5, shuffle=SHUFFLE, compressor="blosclz")
Blosc.isvalidshuffle(shuffle) || throw(ArgumentError("invalid blosc shuffle $shuffle"))
compcode = Blosc.compcode(compressor)
BloscFilter(0,0,0,0,level,shuffle,compcode)
end
Expand All @@ -151,13 +154,17 @@ filter_cfunc(::Type{BloscFilter}) = @cfunction(blosc_filter, Csize_t,
function Base.show(io::IO, blosc::BloscFilter)
print(io, BloscFilter,
"(level=", Int(blosc.level),
",shuffle=", blosc.shuffle!=0,
",shuffle=", blosc.shuffle==NOSHUFFLE ? "NOSHUFFLE" :
blosc.shuffle==SHUFFLE ? "SHUFFLE" :
blosc.shuffle==BITSHUFFLE ? "BITSHUFFLE" :
"UNKNOWN",
",compressor=", Blosc.compname(blosc.compcode),
")")
end

function Base.push!(f::FilterPipeline, blosc::BloscFilter)
0 <= blosc.level <= 9 || throw(ArgumentError("blosc compression $(blosc.level) not in [0,9]"))
Blosc.isvalidshuffle(blosc.shuffle) || throw(ArgumentError("invalid blosc shuffle $(blosc.shuffle)"))
ref = Ref(blosc)
GC.@preserve ref begin
API.h5p_set_filter(f.plist, filterid(BloscFilter), API.H5Z_FLAG_OPTIONAL, div(sizeof(BloscFilter), sizeof(Cuint)), pointer_from_objref(ref))
Expand Down
8 changes: 7 additions & 1 deletion test/filter.jl
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Expand Up @@ -59,6 +59,11 @@ for (name, filter) in compressionFilters

end

ds = create_dataset(
f, "blosc_bitshuffle", datatype(data), dataspace(data),
chunk=(100,100), filters=BloscFilter(shuffle=H5Zblosc.BITSHUFFLE)
)
write(ds, data)

# Close and re-open file for reading
close(f)
Expand All @@ -74,7 +79,8 @@ for name in keys(f)
if startswith(name, "shuffle+")
@test filters[1] isa Shuffle
@test filters[2] isa compressionFilters[name[9:end]]
elseif haskey(compressionFilters, name)
elseif haskey(compressionFilters, name) || name == "blosc_bitshuffle"
name = replace(name, r"_.*"=>"")
@test filters[1] isa compressionFilters[name]
end
end
Expand Down