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Add functionality to skip the four bytes flag and byteswap when read/write extensions #76

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c6829cc
Add functionality to skip the four bytes flag and byteswap when read/…
calvinchai Oct 8, 2024
cf19fba
Add unit tests for extension r/w functions
calvinchai Oct 23, 2024
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2 changes: 1 addition & 1 deletion src/NIfTI.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -232,7 +232,7 @@ Read a NIfTI file to a NIVolume. Set `mmap=true` to memory map the volume.
function niread(file::AbstractString; mmap::Bool=false, mode::AbstractString="r")
io = niopen(file, mode)
hdr, swapped = read_header(io)
ex = read_extensions(io, hdr.vox_offset - 352)
ex = read_extensions(io, hdr.vox_offset - 352, swapbyte=swapped)

if hdr.magic === NP1_MAGIC
vol = read_volume(io, to_eltype(hdr.datatype), to_dimensions(hdr.dim), mmap)
Expand Down
57 changes: 37 additions & 20 deletions src/extensions.jl
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Expand Up @@ -141,42 +141,59 @@ function esize(ex::NIfTIExtension)
return ret
end

function read_extensions(io, n)
function read_extensions(io, n; swapbyte::Bool=false, skip_extension_flag::Bool=false)
ret = NIfTIExtension[]
if eof(io)
return ret
else
end

if !skip_extension_flag
b1 = read(io, UInt8)
# GZIP doesn't skip so we read and throw away
read(io, UInt8)
read(io, UInt8)
read(io, UInt8)
if b1 === zero(UInt8)
return ret
else
counter = 0
while counter < (n - 1)
esize = read(io, Int32)
ec = read(io, Int32)
push!(ret, NIfTIExtension(ec, read!(io, Array{UInt8}(undef, esize - 8))))
counter += esize
end
return ret
end
end

swap_int32 = swapbyte ? bswap : x -> x
counter = skip_extension_flag ? 0 : 4
while counter < (n - 1)
esize = swap_int32(read(io, Int32))
ec = swap_int32(read(io, Int32))
push!(ret, NIfTIExtension(ec, read!(io, Array{UInt8}(undef, esize - 8))))
counter += esize
end
return ret

end

write(path::AbstractString, x::Vector{NIfTIExtension}; swapbyte::Bool=false, skip_extension_flag::Bool=false) =
open(path, "w") do io
write(io, x, swapbyte=swapbyte, skip_extension_flag=skip_extension_flag)
end

function write(io::IO, x::Vector{NIfTIExtension})
function write(io::IO, x::Vector{NIfTIExtension}; swapbyte::Bool=false, skip_extension_flag::Bool=false)
if isempty(x)
write(io, fill(UInt8(0), 4))
else
write(io, UInt8[1, 0, 0, 0])
for ex in x
write(io, Int32(esize(ex)))
write(io, ex.ecode)
write(io, ex.edata)
# write(io, zeros(UInt8, esize(ex) - length(ex.edata)))
if !skip_extension_flag
write(io, fill(UInt8(0), 4))
end
return
end
if !skip_extension_flag
write(io, UInt8[1, 0, 0, 0])
end

swap_int32 = swapbyte ? bswap : x -> x

for ex in x
write(io, swap_int32(Int32(esize(ex))))
write(io, swap_int32(ex.ecode))
write(io, ex.edata)
# write(io, zeros(UInt8, esize(ex) - length(ex.edata)))
end

end

71 changes: 50 additions & 21 deletions test/runtests.jl
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Expand Up @@ -52,17 +52,17 @@ function image_tests(fname, mmap)
@assert maximum(img) == maximum(img.raw)

@test getaffine(img) ≈ [
-2.0 6.714715653593746e-19 9.081024511081715e-18 117.8551025390625
6.714715653593746e-19 1.9737114906311035 -0.35552823543548584 -35.72294235229492
8.25548088896093e-18 0.3232076168060303 2.171081781387329 -7.248798370361328
0.0 0.0 0.0 1.0
-2.0 6.714715653593746e-19 9.081024511081715e-18 117.8551025390625
6.714715653593746e-19 1.9737114906311035 -0.35552823543548584 -35.72294235229492
8.25548088896093e-18 0.3232076168060303 2.171081781387329 -7.248798370361328
0.0 0.0 0.0 1.0
]

@test NIfTI.get_qform(img) ≈ [
-2.0 7.75482f-26 -6.93824f-27 117.855
7.75482f-26 1.97371 -0.355528 -35.7229
6.30749f-27 0.323208 2.17108 -7.2488
0.0 0.0 0.0 1.0
-2.0 7.75482f-26 -6.93824f-27 117.855
7.75482f-26 1.97371 -0.355528 -35.7229
6.30749f-27 0.323208 2.17108 -7.2488
0.0 0.0 0.0 1.0
]
@test NIfTI.orientation(img) == (:right, :posterior, :inferior)
end
Expand Down Expand Up @@ -118,30 +118,59 @@ const WRITE = joinpath(TEMP_DIR_NAME, "$(tempname()).nii")
const VERIFY_WRITE = joinpath(TEMP_DIR_NAME, "$(tempname()).nii")
cp(NII, WRITE)
img = niread(WRITE; mmap=true, mode="r+")
img.raw[1,1,1,1] = 5
img.raw[:,2,1,1] = ones(size(img)[1])
img.raw[1, 1, 1, 1] = 5
img.raw[:, 2, 1, 1] = ones(size(img)[1])
cp(WRITE, VERIFY_WRITE)
@test niread(VERIFY_WRITE)[1,1,1,1] == 5
@test niread(VERIFY_WRITE)[:,2,1,1] == ones(size(img)[1])
@test niread(VERIFY_WRITE)[1, 1, 1, 1] == 5
@test niread(VERIFY_WRITE)[:, 2, 1, 1] == ones(size(img)[1])
# Site is currently down TODO: reintroduce this test when site is up
# Big endian
# const BE = "$(tempname()).nii"
# download("https://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.nii.gz", BE)
img = niread(joinpath(dirname(@__FILE__), "data/avg152T1_LR_nifti.nii.gz"))
@test size(img) == (91,109,91)
@test size(img) == (91, 109, 91)

GC.gc() # closes mmapped files

@test NIfTI._dir2ori(-1.0, 0.0, 0.0,
0.0, 1.0, 0.0,
0.0, 0.0, 1.0) == (:right, :posterior, :inferior)
0.0, 1.0, 0.0,
0.0, 0.0, 1.0) == (:right, :posterior, :inferior)

@test NIfTI._dir2ori(1.0, 0.0, 0.0,
0.0, -1.0, 0.0,
0.0, 0.0, 1.0) == (:left, :anterior, :inferior)
@test NIfTI._dir2ori(1.0, 0.0, 0.0,
0.0, -1.0, 0.0,
0.0, 0.0, 1.0) == (:left, :anterior, :inferior)


@test NIfTI._dir2ori(1.0, 0.0, 0.0,
0.0, -1.0, 0.0,
0.0, 0.0, -1.0) == (:left, :anterior, :superior)
@test NIfTI._dir2ori(1.0, 0.0, 0.0,
0.0, -1.0, 0.0,
0.0, 0.0, -1.0) == (:left, :anterior, :superior)


@testset "Extension Read Write" begin
img = niread(GZIPPED_NII)
temp_bin = "$(tempname()).bin"
NIfTI.write(temp_bin, img.extensions)
extensions = NIfTI.read_extensions(open(temp_bin), 68)
fd = open(temp_bin, "r")
chunk = read(fd, Int32)
sys_order_size = read(fd, Int32)
sys_order_ecode = read(fd, Int32)
close(fd)
@test (chunk == 1 || chunk == bswap(Int32(1)))
@test sys_order_size == 32
@test extensions[1].ecode == sys_order_ecode

NIfTI.write(temp_bin, img.extensions, swapbyte=true, skip_extension_flag=true)

fd = open(temp_bin, "r")
reverse_order_size = read(fd, Int32)
reverse_order_ecode = read(fd, Int32)
close(fd)
extensions = NIfTI.read_extensions(open(temp_bin), 64, swapbyte=true, skip_extension_flag=true)
@test extensions[1].ecode == sys_order_ecode

@test reverse_order_size == bswap(Int32(sys_order_size))
@test reverse_order_ecode == bswap(Int32(sys_order_ecode))
end


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