depot/third_party/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix

70 lines
2 KiB
Nix

{ 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 (finalAttrs: {
version = "1.0.20240202";
pname = "dcm2niix";
src = fetchFromGitHub {
owner = "rordenlab";
repo = "dcm2niix";
rev = "v${finalAttrs.version}";
sha256 = "sha256-vJUPv/6KNCsU8UjwfktHdTlsweG7+UGgAEZeESfBkD8=";
};
patches = lib.optionals withCloudflareZlib [
(substituteAll {
src = ./dont-fetch-external-libs.patch;
inherit cloudflareZlib;
})
];
nativeBuildInputs = [ cmake ];
buildInputs = lib.optionals batchVersion [ yaml-cpp ]
++ lib.optionals withOpenJpeg [ openjpeg openjpeg.dev ];
cmakeFlags = lib.optionals batchVersion [
"-DBATCH_VERSION=ON"
"-DYAML-CPP_DIR=${yaml-cpp}/lib/cmake/yaml-cpp"
] ++ lib.optionals withJpegLs [
"-DUSE_JPEGLS=ON"
] ++ lib.optionals withOpenJpeg [
"-DUSE_OPENJPEG=ON"
"-DOpenJPEG_DIR=${openjpeg}/lib/${openjpeg.pname}-${lib.versions.majorMinor openjpeg.version}"
] ++ lib.optionals withCloudflareZlib [
"-DZLIB_IMPLEMENTATION=Cloudflare"
];
meta = {
description = "DICOM to NIfTI converter";
mainProgram = "dcm2niix";
longDescription = ''
dcm2niix is designed to convert neuroimaging data from the DICOM format to the NIfTI format.
'';
homepage = "https://www.nitrc.org/projects/dcm2nii";
changelog = "https://github.com/rordenlab/dcm2niix/releases/tag/v${finalAttrs.version}";
license = lib.licenses.bsd3;
maintainers = with lib.maintainers; [ ashgillman rbreslow ];
platforms = lib.platforms.all;
};
})