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Merge pull request #265927 from bcdarwin/itk-unvendor

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itk: unvendor some of the dependencies
This commit is contained in:
Mario Rodas 2023-11-21 08:33:54 -05:00 committed by GitHub
parent b56dc6becd dc16ee7014
commit dba8a3ef92
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GPG key ID: 4AEE18F83AFDEB23
2 changed files with 34 additions and 11 deletions
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2
pkgs/development/libraries/gdcm/default.nix
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@ -76,6 +76,8 @@ stdenv.mkDerivation rec {
"TestSCUValidation"
# errors because 3 classes not wrapped:
"TestWrapPython"
] ++ lib.optionals (stdenv.isAarch64 && stdenv.isLinux) [
"TestRescaler2"
];
checkPhase = ''

43
pkgs/development/libraries/itk/generic.nix
View file

@ -1,7 +1,8 @@
{ version, rev, sourceSha256 }:
{ lib, stdenv, fetchFromGitHub, cmake, makeWrapper
, pkg-config, libX11, libuuid, xz, vtk, Cocoa }:
{ lib, stdenv, fetchFromGitHub, cmake
, expat, fftw, gdcm, hdf5-cpp, libjpeg, libminc, libtiff, libpng
, libX11, libuuid, xz, vtk, zlib, Cocoa }:
let
itkGenericLabelInterpolatorSrc = fetchFromGitHub {
@ -41,8 +42,6 @@ stdenv.mkDerivation {
substituteInPlace CMake/ITKSetStandardCompilerFlags.cmake \
--replace "-march=corei7" "" \
--replace "-mtune=native" ""
substituteInPlace Modules/ThirdParty/GDCM/src/gdcm/Utilities/gdcmopenjpeg/src/lib/openjp2/libopenjp2.pc.cmake.in \
--replace "@OPENJPEG_INSTALL_LIB_DIR@" "@OPENJPEG_INSTALL_FULL_LIB_DIR@"
ln -sr ${itkGenericLabelInterpolatorSrc} Modules/External/ITKGenericLabelInterpolator
ln -sr ${itkAdaptiveDenoisingSrc} Modules/External/ITKAdaptiveDenoising
ln -sr ${itkSimpleITKFiltersSrc} Modules/External/ITKSimpleITKFilters
@ -52,6 +51,15 @@ stdenv.mkDerivation {
"-DBUILD_EXAMPLES=OFF"
"-DBUILD_SHARED_LIBS=ON"
"-DITK_FORBID_DOWNLOADS=ON"
"-DITK_USE_SYSTEM_LIBRARIES=ON" # finds common libraries e.g. hdf5, libpng, libtiff, zlib, but not GDCM, NIFTI, MINC, etc.
# note ITK_USE_SYSTEM_EIGEN, part of ITK_USE_SYSTEM_LIBRARIES,
# causes "...-itk-5.2.1/include/ITK-5.2/itkSymmetricEigenAnalysis.h:23:31: fatal error: Eigen/Eigenvalues: No such file or directory"
# when compiling c3d, but maybe an ITK 5.2/eigen version issue:
"-DITK_USE_SYSTEM_EIGEN=OFF"
"-DITK_USE_SYSTEM_GOOGLETEST=OFF" # ANTs build failure due to https://github.com/ANTsX/ANTs/issues/1489
"-DITK_USE_SYSTEM_GDCM=ON"
"-DITK_USE_SYSTEM_MINC=ON"
"-DLIBMINC_DIR=${libminc}/lib/cmake"
"-DModule_ITKMINC=ON"
"-DModule_ITKIOMINC=ON"
"-DModule_ITKIOTransformMINC=ON"
@ -63,8 +71,12 @@ stdenv.mkDerivation {
"-DModule_GenericLabelInterpolator=ON"
];
nativeBuildInputs = [ cmake xz makeWrapper ];
buildInputs = [ libX11 libuuid vtk ] ++ lib.optionals stdenv.isDarwin [ Cocoa ];
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
@ -72,11 +84,20 @@ stdenv.mkDerivation {
# 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 = vtk.propagatedBuildInputs;
postInstall = ''
wrapProgram "$out/bin/h5c++" --prefix PATH ":" "${pkg-config}/bin"
'';
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";