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{ version, rev, sourceSha256 }:
{ lib, stdenv, fetchFromGitHub, fetchpatch, cmake
, expat, fftw, gdcm, hdf5-cpp, libjpeg, libminc, libtiff, libpng
, libX11, libuuid, xz, vtk, zlib, Cocoa }:
let
itkGenericLabelInterpolatorSrc = fetchFromGitHub {
owner = "InsightSoftwareConsortium";
repo = "ITKGenericLabelInterpolator";
rev = "2f3768110ffe160c00c533a1450a49a16f4452d9";
hash = "sha256-Cm3jg14MMnbr/sP+gqR2Rh25xJjoRvpmY/jP/DKH978=";
};
itkAdaptiveDenoisingSrc = fetchFromGitHub {
owner = "ntustison";
repo = "ITKAdaptiveDenoising";
rev = "24825c8d246e941334f47968553f0ae388851f0c";
hash = "sha256-deJbza36c0Ohf9oKpO2T4po37pkyI+2wCSeGL4r17Go=";
};
itkSimpleITKFiltersSrc = fetchFromGitHub {
owner = "InsightSoftwareConsortium";
repo = "ITKSimpleITKFilters";
rev = "bb896868fc6480835495d0da4356d5db009592a6";
hash = "sha256-MfaIA0xxA/pzUBSwnAevr17iR23Bo5iQO2cSyknS3o4=";
};
in
stdenv.mkDerivation {
pname = "itk";
inherit version;
src = fetchFromGitHub {
owner = "InsightSoftwareConsortium";
repo = "ITK";
inherit rev;
sha256 = sourceSha256;
};
patches = [
(fetchpatch {
name = "fix-gcc13-build";
url = "https://github.com/InsightSoftwareConsortium/ITK/commit/9a719a0d2f5f489eeb9351b0ef913c3693147a4f.patch";
hash = "sha256-dDyqYOzo91afR8W7k2N64X6l7t6Ws1C9iuRkWHUe0fg=";
})
];
postPatch = ''
substituteInPlace CMake/ITKSetStandardCompilerFlags.cmake \
--replace "-march=corei7" "" \
--replace "-mtune=native" ""
ln -sr ${itkGenericLabelInterpolatorSrc} Modules/External/ITKGenericLabelInterpolator
ln -sr ${itkAdaptiveDenoisingSrc} Modules/External/ITKAdaptiveDenoising
ln -sr ${itkSimpleITKFiltersSrc} Modules/External/ITKSimpleITKFilters
'';
cmakeFlags = [
"-DBUILD_EXAMPLES=OFF"
"-DBUILD_SHARED_LIBS=ON"
"-DITK_FORBID_DOWNLOADS=ON"
"-DITK_USE_SYSTEM_LIBRARIES=ON" # finds common libraries e.g. hdf5, libpng, libtiff, zlib, but not GDCM, NIFTI, MINC, etc.
# note ITK_USE_SYSTEM_EIGEN, part of ITK_USE_SYSTEM_LIBRARIES,
# causes "...-itk-5.2.1/include/ITK-5.2/itkSymmetricEigenAnalysis.h:23:31: fatal error: Eigen/Eigenvalues: No such file or directory"
# when compiling c3d, but maybe an ITK 5.2/eigen version issue:
"-DITK_USE_SYSTEM_EIGEN=OFF"
"-DITK_USE_SYSTEM_GOOGLETEST=OFF" # ANTs build failure due to https://github.com/ANTsX/ANTs/issues/1489
"-DITK_USE_SYSTEM_GDCM=ON"
"-DITK_USE_SYSTEM_MINC=ON"
"-DLIBMINC_DIR=${libminc}/lib/cmake"
"-DModule_ITKMINC=ON"
"-DModule_ITKIOMINC=ON"
"-DModule_ITKIOTransformMINC=ON"
"-DModule_SimpleITKFilters=ON"
"-DModule_ITKVtkGlue=ON"
"-DModule_ITKReview=ON"
"-DModule_MGHIO=ON"
"-DModule_AdaptiveDenoising=ON"
"-DModule_GenericLabelInterpolator=ON"
];
nativeBuildInputs = [ cmake xz ];
buildInputs = [
libX11
libuuid
vtk
] ++ lib.optionals stdenv.isDarwin [ Cocoa ];
# Due to ITKVtkGlue=ON and the additional dependencies needed to configure VTK 9
# (specifically libGL and libX11 on Linux),
# it's now seemingly necessary for packages that configure ITK to
# also include configuration deps of VTK, even if VTK is not required or available.
# These deps were propagated from VTK 9 in https://github.com/NixOS/nixpkgs/pull/206935,
# so we simply propagate them again from ITK.
# This admittedly is a hack and seems like an issue with VTK 9's CMake configuration.
propagatedBuildInputs = [
# The dependencies we've un-vendored from ITK, such as GDCM, must be propagated,
# otherwise other software built against ITK fails to configure since ITK headers
# refer to these previously vendored libraries:
expat
fftw
gdcm
hdf5-cpp
libjpeg
libminc
libpng
libtiff
zlib
] ++ vtk.propagatedBuildInputs;
meta = {
description = "Insight Segmentation and Registration Toolkit";
homepage = "https://www.itk.org";
license = lib.licenses.asl20;
maintainers = with lib.maintainers; [viric];
};
}
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