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Reference Implementation: Julia #3

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Reference Implementation: Julia #3

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df9f9ec
WIP: julia implementation
balbasty Dec 16, 2023
28759f2
very early WIP -- not working
balbasty Dec 29, 2023
2b7c323
FIXES(julia/nii2zarr): conversion runs through without erroring (did …
balbasty Dec 29, 2023
c40c09f
FIXES(julia): now seems to work
balbasty Jan 2, 2024
0c900db
DOC(julia): add README
balbasty Jan 2, 2024
4e14053
DOC(julia): use correct highlighting
balbasty Jan 2, 2024
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24 changes: 24 additions & 0 deletions julia/NIfTIZarr.jl/.gitignore
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# Files generated by invoking Julia with --code-coverage
*.jl.cov
*.jl.*.cov

# Files generated by invoking Julia with --track-allocation
*.jl.mem

# System-specific files and directories generated by the BinaryProvider and BinDeps packages
# They contain absolute paths specific to the host computer, and so should not be committed
deps/deps.jl
deps/build.log
deps/downloads/
deps/usr/
deps/src/

# Build artifacts for creating documentation generated by the Documenter package
docs/build/
docs/site/

# File generated by Pkg, the package manager, based on a corresponding Project.toml
# It records a fixed state of all packages used by the project. As such, it should not be
# committed for packages, but should be committed for applications that require a static
# environment.
Manifest.toml
22 changes: 22 additions & 0 deletions julia/NIfTIZarr.jl/Project.toml
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name = "NIfTIZarr"
uuid = "37a98a6a-6d49-420d-b818-2675248c7c06"
authors = ["Yael Balbastre <[email protected]>"]
version = "0.1.0"

[deps]
Base64 = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
Zarr = "0a941bbe-ad1d-11e8-39d9-ab76183a1d99"
NIfTI = "a3a9e032-41b5-5fc4-967a-a6b7a19844d3"
EnumX = "4e289a0a-7415-4d19-859d-a7e5c4648b56"
Images = "916415d5-f1e6-5110-898d-aaa5f9f070e0"
Formatting = "59287772-0a20-5a39-b81b-1366585eb4c0"
LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
GZip = "92fee26a-97fe-5a0c-ad85-20a5f3185b63"
StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"

[compat] # to check
Zarr = "0.7" # storage API change (added path)
NIfTI = "0.6"
EnumX = "1.0"
Images = ">=0.8"
julia = "1.6"
21 changes: 21 additions & 0 deletions julia/NIfTIZarr.jl/README.md
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# Example implementation of the nifti-zarr specification in JULIA

Convert a nifti file to a nifti-zarr storage.
```julia
import NIfTIZarr: nii2zarr
nii2zarr("path/to/nifti.nii.gz", "s3://path/to/bucket")
```

Convert a nifti-zarr storage to a nifti file.
The pyramid level can be selected with `level=L`, where 0 is the
base/finest level.
```julia
import NIfTIZarr: zarr2nii
zarr2nii("s3://path/to/bucket", "path/to/nifti.nii.gz"; level=0)
```

Load a nifti-zarr into a `NIVolume` object.
```julia
import NIfTIZarr: zarr2nii
nivol = zarr2nii("s3://path/to/bucket"; level=0)
```
246 changes: 246 additions & 0 deletions julia/NIfTIZarr.jl/notebooks/conversion.ipynb
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{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"\u001b[32m\u001b[1m Resolving\u001b[22m\u001b[39m package versions...\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\u001b[32m\u001b[1m No Changes\u001b[22m\u001b[39m to `~/Dropbox (Partners HealthCare)/code/balbasty/nifti-zarr/Project.toml`\n",
"\u001b[32m\u001b[1m No Changes\u001b[22m\u001b[39m to `~/Dropbox (Partners HealthCare)/code/balbasty/nifti-zarr/Manifest.toml`\n"
]
}
],
"source": [
"import Pkg\n",
"Pkg.develop(path=\"..\")\n",
"\n",
"import NIfTIZarr: nii2zarr, zarr2nii\n"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"\"/Users/yb947/Dropbox/data/niizarr/sub-control01_T1w_level1_julia.nii.gz\""
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"PATH_NII = \"$(homedir())/Dropbox/data/niizarr/sub-control01_T1w.nii.gz\"\n",
"PATH_ZARR = \"$(homedir())/Dropbox/data/niizarr/sub-control01_T1w_julia.nii.zarr\"\n",
"PATH_NII0 = \"$(homedir())/Dropbox/data/niizarr/sub-control01_T1w_level0_julia.nii.gz\"\n",
"PATH_NII1 = \"$(homedir())/Dropbox/data/niizarr/sub-control01_T1w_level1_julia.nii.gz\"\n"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"Base.Filesystem.rm(PATH_ZARR; recursive=true, force=true)\n",
"nii2zarr(PATH_NII, PATH_ZARR)\n"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"┌ Warning: In the future, fill values will not be interpreted as missing values by default. \n",
"│ Please set the keyword argument `fill_as_missing` to a boolean accordingly. Setting to `true`\n",
"│ for now, but in the future `false` will be the default.\n",
"└ @ Zarr /Users/yb947/.julia/packages/Zarr/tmr2s/src/metadata.jl:182\n",
"┌ Warning: In the future, fill values will not be interpreted as missing values by default. \n",
"│ Please set the keyword argument `fill_as_missing` to a boolean accordingly. Setting to `true`\n",
"│ for now, but in the future `false` will be the default.\n",
"└ @ Zarr /Users/yb947/.julia/packages/Zarr/tmr2s/src/metadata.jl:182\n"
]
},
{
"data": {
"text/plain": [
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"[:, :, 1] =\n",
" 1.357 1.59278 1.15461 1.40221 … 3.2627 4.23032 3.92529 2.51416\n",
" 1.68678 1.76973 1.63274 1.56868 3.49257 3.68682 3.93434 2.07428\n",
" 1.45721 1.63145 1.58165 1.4172 4.13475 4.79732 4.6226 2.42931\n",
" 1.69925 1.46471 1.43601 1.36439 4.57429 4.97035 4.39584 2.29437\n",
" 1.40136 1.27899 1.33121 1.36919 4.2912 4.70872 4.2165 2.45473\n",
" 1.28602 1.24542 1.21639 1.54462 … 3.9789 4.11125 4.73422 3.51948\n",
" 1.22865 1.36626 1.30932 1.46237 3.72477 4.11917 4.29881 3.00019\n",
" 1.08642 1.22378 1.30596 1.29892 4.06885 4.24407 4.29809 2.98617\n",
" 1.15746 1.05802 1.19913 1.18579 4.89318 4.60041 4.39017 2.49266\n",
" 1.59305 1.64865 2.07987 1.827 4.77972 4.62573 4.90107 2.39773\n",
" ⋮ ⋱ ⋮ \n",
" 1.8988 2.04685 1.68634 1.83424 2.39405 2.95284 2.76905 1.80408\n",
" 2.95865 2.87626 1.94597 1.84225 … 2.37085 2.87516 2.81667 2.07517\n",
" 3.69512 2.89118 1.91726 1.83967 2.42435 2.53215 3.40241 3.85031\n",
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"\n",
"[:, :, 2] =\n",
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" 1.86673 1.48315 1.89374 1.95869 4.12345 3.98642 3.8535 2.27323\n",
" ⋮ ⋱ ⋮ \n",
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" 1.49186 1.6004 1.77617 1.86036 2.15884 2.24682 2.20466 1.30258\n",
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" 1.75215 1.71188 1.76014 1.68292 2.10476 2.61619 2.31862 1.53551\n",
" 1.41662 1.50966 1.65199 1.72882 2.17255 2.29342 2.56416 1.2272\n",
"\n",
"[:, :, 3] =\n",
" 1.45447 1.39946 1.71497 1.72248 … 3.23837 2.86939 2.97971 1.75254\n",
" 1.588 1.47563 1.56445 1.59111 3.42411 3.29554 3.78897 2.2778\n",
" 1.52613 1.6936 1.62732 1.45715 3.06856 3.47821 3.60062 1.93519\n",
" 1.68487 1.38851 1.50072 1.54873 2.98044 3.74508 3.63863 2.15971\n",
" 1.4906 1.3778 1.59961 1.54661 3.50072 4.12115 4.39875 3.27381\n",
" 1.62444 1.37224 1.69886 1.52737 … 3.38672 3.892 4.23806 2.81283\n",
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" 1.77913 2.18913 2.15865 2.09737 4.02312 3.98434 3.88309 2.59335\n",
" ⋮ ⋱ ⋮ \n",
" 1.9207 1.68214 1.43685 1.63338 2.86951 2.80342 2.56119 1.38803\n",
" 1.81444 1.8355 1.26882 1.2588 … 2.55888 2.91637 2.87506 1.41316\n",
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" 2.1019 1.92472 1.94874 1.9252 2.27987 2.62855 2.31835 1.31463\n",
"\n",
";;; … \n",
"\n",
"[:, :, 126] =\n",
" 0.948734 0.883659 1.00251 … 1.30374 1.06609 1.20856 0.7441\n",
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" 1.02364 1.06139 1.04602 1.4445 1.35153 1.13683 0.714981\n",
" ⋮ ⋱ ⋮ \n",
" 1.16879 1.14239 1.29535 1.23177 1.00725 1.2816 0.733979\n",
" 1.22908 1.05818 1.1717 … 1.30682 1.05041 1.0543 0.602555\n",
" 1.15152 0.916998 1.10414 1.27151 1.09899 1.14741 0.615706\n",
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" 1.2532 1.08641 1.01581 1.16314 1.51612 1.42116 0.863436\n",
"\n",
"[:, :, 127] =\n",
" 0.961934 1.01625 1.39392 1.33686 … 1.14224 1.34796 0.633942\n",
" 0.955435 1.12264 1.05252 1.31089 1.61212 1.72255 0.755992\n",
" 1.06604 0.990939 0.982047 1.50945 1.78166 1.92994 0.888357\n",
" 1.01792 1.11335 0.967425 1.23839 1.60884 1.4728 0.914809\n",
" 1.20744 1.34394 1.03329 1.08042 1.49726 1.5207 1.01235\n",
" 1.41233 1.07854 1.13411 1.28756 … 1.34038 1.50595 0.87348\n",
" 1.0639 0.942872 0.89819 1.03062 1.55421 1.32355 0.74044\n",
" 0.913582 1.0451 1.0208 0.976221 1.39133 1.3779 0.878592\n",
" 1.02216 1.09259 1.04501 0.996944 1.3139 1.28093 0.86989\n",
" 1.03489 1.05262 1.10897 1.01842 1.3184 1.09564 0.746787\n",
" ⋮ ⋱ ⋮ \n",
" 1.33144 1.10893 1.28263 1.4355 1.10776 1.27297 0.62796\n",
" 1.31673 1.0354 1.28069 1.20425 … 1.03677 1.17098 0.687918\n",
" 1.2214 1.2452 1.35566 0.993172 1.16286 1.24002 0.838187\n",
" 1.19516 1.06936 1.18436 1.08582 1.40989 1.34841 0.83577\n",
" 0.918455 1.18751 1.16187 1.10403 1.22639 1.34132 0.642707\n",
" 0.913276 1.23535 1.29452 1.07763 0.989565 1.10117 0.598383\n",
" 1.18587 1.29838 1.30831 1.16317 … 1.27463 1.27353 0.777536\n",
" 1.21928 0.961139 0.986386 1.06376 1.35767 1.17591 0.690446\n",
" 1.267 1.20985 1.30839 1.10933 1.41515 1.34566 0.983026\n",
"\n",
"[:, :, 128] =\n",
" 0.535765 0.631842 0.822765 0.706593 … 0.674699 0.849007 0.470105\n",
" 0.481257 0.502498 0.599324 0.690372 0.823602 0.987125 0.565625\n",
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" 0.492043 0.627576 0.826248 0.669414 0.661946 0.558626 0.394894\n",
" ⋮ ⋱ ⋮ \n",
" 0.660428 0.722206 0.60854 0.632177 0.713089 0.713276 0.337343\n",
" 0.646061 0.589514 0.686182 0.624146 … 0.718902 0.58754 0.312289\n",
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" 0.598762 0.7442 0.697167 0.520344 0.825367 0.819818 0.32897\n",
" 0.45521 0.61518 0.587057 0.568058 0.580297 0.760701 0.456735\n",
" 0.509076 0.574354 0.5325 0.602875 … 0.783706 0.885157 0.480425\n",
" 0.563556 0.508574 0.539496 0.656335 0.804593 0.762366 0.472935\n",
" 0.456855 0.685933 0.893084 0.730634 0.692565 0.681531 0.536124"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"zarr2nii(PATH_ZARR, PATH_NII0; level=0)\n",
"zarr2nii(PATH_ZARR, PATH_NII1; level=1)"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Julia 1.8.3",
"language": "julia",
"name": "julia-1.8"
},
"language_info": {
"file_extension": ".jl",
"mimetype": "application/julia",
"name": "julia",
"version": "1.8.3"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
10 changes: 10 additions & 0 deletions julia/NIfTIZarr.jl/src/NIfTIZarr.jl
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module NIfTIZarr

include("header.jl")
include("affines.jl")
include("nii2zarr.jl")
include("zarr2nii.jl")

export nii2json, nii2zarr

end # module
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