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{ lib
, stdenv
, fetchFromGitHub
, substituteAll
, cmake
, openjpeg
, yaml-cpp
, batchVersion ? false
, withJpegLs ? true
, withOpenJpeg ? true
, withCloudflareZlib ? true
}:
let
cloudflareZlib = fetchFromGitHub {
owner = "ningfei";
repo = "zlib";
# HEAD revision of the gcc.amd64 branch on 2023-03-28. Reminder to update
# whenever bumping package version.
rev = "f49b13c3380cf9677ae9a93641ebc6f770899def";
sha256 = "sha256-8HNFUGx2uuEb8UrGUiqkN+uVDX83YIisT2uO1Z7GCxc=";
};
in
stdenv.mkDerivation rec {
version = "1.0.20230411";
pname = "dcm2niix";
src = fetchFromGitHub {
owner = "rordenlab";
repo = "dcm2niix";
rev = "v${version}";
sha256 = "sha256-kOVEoqrk4l6sH8iDVx1QmOYP5tCufxsWnCnn9BibZ08=";
};
patches = lib.optionals withCloudflareZlib [
(substituteAll {
src = ./dont-fetch-external-libs.patch;
inherit cloudflareZlib;
})
];
nativeBuildInputs = [ cmake ];
buildInputs = lib.optionals batchVersion [ yaml-cpp ]
++ lib.optionals withOpenJpeg [ openjpeg openjpeg.dev ];
cmakeFlags = lib.optionals batchVersion [
"-DBATCH_VERSION=ON"
"-DYAML-CPP_DIR=${yaml-cpp}/lib/cmake/yaml-cpp"
] ++ lib.optionals withJpegLs [
"-DUSE_JPEGLS=ON"
] ++ lib.optionals withOpenJpeg [
"-DUSE_OPENJPEG=ON"
"-DOpenJPEG_DIR=${openjpeg}/lib/${openjpeg.pname}-${lib.versions.majorMinor openjpeg.version}"
] ++ lib.optionals withCloudflareZlib [
"-DZLIB_IMPLEMENTATION=Cloudflare"
];
meta = with lib; {
description = "DICOM to NIfTI converter";
longDescription = ''
dcm2niix is designed to convert neuroimaging data from the DICOM format to the NIfTI format.
'';
homepage = "https://www.nitrc.org/projects/dcm2nii";
license = licenses.bsd3;
maintainers = with maintainers; [ ashgillman rbreslow ];
platforms = platforms.all;
};
}
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