From 06fc8aa4dc99aa1387566ffee212f2b27bb5c6bf Mon Sep 17 00:00:00 2001 From: Ben Darwin Date: Fri, 23 Aug 2024 14:17:17 -0400 Subject: [PATCH] python312Packages.itk: init at 5.4.0 --- pkgs/development/libraries/itk/generic.nix | 124 ++++++++++++++------ pkgs/development/libraries/itk/itk.egg-info | 5 + pkgs/top-level/python-packages.nix | 8 +- 3 files changed, 103 insertions(+), 34 deletions(-) create mode 100644 pkgs/development/libraries/itk/itk.egg-info diff --git a/pkgs/development/libraries/itk/generic.nix b/pkgs/development/libraries/itk/generic.nix index b7ff7292dc23..7ac9d6d8fbfe 100644 --- a/pkgs/development/libraries/itk/generic.nix +++ b/pkgs/development/libraries/itk/generic.nix @@ -10,6 +10,8 @@ fetchFromGitHub, fetchpatch, cmake, + castxml, + swig, expat, fftw, gdcm, @@ -20,13 +22,21 @@ libpng, libX11, libuuid, + patchelf, + python ? null, + numpy ? null, xz, vtk, + which, zlib, Cocoa, + enablePython ? false, }: let + # Python wrapper contains its own VTK support incompatible with MODULE_ITKVtkGlue + withVtk = !enablePython; + itkGenericLabelInterpolatorSrc = fetchFromGitHub { owner = "InsightSoftwareConsortium"; repo = "ITKGenericLabelInterpolator"; @@ -47,6 +57,19 @@ let rev = "bb896868fc6480835495d0da4356d5db009592a6"; hash = "sha256-MfaIA0xxA/pzUBSwnAevr17iR23Bo5iQO2cSyknS3o4="; }; + + # remove after next swig update: + swigUnstable = swig.overrideAttrs ({ + version = "4.2.1-unstable-2024-08-19"; + + src = fetchFromGitHub { + owner = "swig"; + repo = "swig"; + rev = "5ac5d90f970759fbe705fae551d0743a7c63c67e"; + hash = "sha256-32EFLHpP4l04nqrc8dt4Qsr8deTBqLt8lUlhnNnaIGU="; + }; + + }); in stdenv.mkDerivation { @@ -77,39 +100,56 @@ stdenv.mkDerivation { 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" - ]; + 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=${libminc}/lib/cmake" + "-DModule_ITKMINC=ON" + "-DModule_ITKIOMINC=ON" + "-DModule_ITKIOTransformMINC=ON" + "-DModule_SimpleITKFilters=ON" + "-DModule_ITKReview=ON" + "-DModule_MGHIO=ON" + "-DModule_AdaptiveDenoising=ON" + "-DModule_GenericLabelInterpolator=ON" + ] + ++ lib.optionals enablePython [ + "-DITK_WRAP_PYTHON=ON" + "-DITK_USE_SYSTEM_CASTXML=ON" + "-DITK_USE_SYSTEM_SWIG=ON" + "-DPY_SITE_PACKAGES_PATH=${placeholder "out"}/${python.sitePackages}" + ] + ++ lib.optionals withVtk [ "-DModule_ITKVtkGlue=ON" ]; - nativeBuildInputs = [ - cmake - xz - ]; - buildInputs = [ - libX11 - libuuid - vtk - ] ++ lib.optionals stdenv.isDarwin [ Cocoa ]; + nativeBuildInputs = + [ + cmake + xz + ] + ++ lib.optionals enablePython [ + castxml + swigUnstable + which + ]; + + buildInputs = + [ + libX11 + libuuid + ] + ++ lib.optionals stdenv.isDarwin [ Cocoa ] + ++ lib.optionals enablePython [ python ] + ++ lib.optionals withVtk [ vtk ]; # 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 @@ -130,12 +170,30 @@ stdenv.mkDerivation { libpng libtiff zlib - ] ++ vtk.propagatedBuildInputs; + ] ++ lib.optionals withVtk vtk.propagatedBuildInputs ++ lib.optionals enablePython [ numpy ]; + + postInstall = lib.optionalString enablePython '' + substitute \ + ${./itk.egg-info} \ + $out/${python.sitePackages}/itk-${version}.egg-info \ + --subst-var-by ITK_VER "${version}" + ''; + + # remove forbidden reference to /build which occur when building the Python wrapping + # (also remove a copy of itkTestDriver with incorrect permissions/RPATH): + preFixup = lib.optionals enablePython '' + rm $out/${python.sitePackages}/itk/itkTestDriver + find $out/${python.sitePackages}/itk -type f -name '*.so*' -exec \ + patchelf {} --shrink-rpath --allowed-rpath-prefixes "$NIX_STORE" \; + ''; meta = { description = "Insight Segmentation and Registration Toolkit"; homepage = "https://www.itk.org"; license = lib.licenses.asl20; maintainers = with lib.maintainers; [ bcdarwin ]; + # aarch64-linux Python wrapping fails with "error: unknown type name '_Float128'" and similar; + # compilation runs slowly and times out on Darwin + platforms = with lib.platforms; if enablePython then [ "x86_64-linux" ] else unix; }; } diff --git a/pkgs/development/libraries/itk/itk.egg-info b/pkgs/development/libraries/itk/itk.egg-info new file mode 100644 index 000000000000..2c523ec27848 --- /dev/null +++ b/pkgs/development/libraries/itk/itk.egg-info @@ -0,0 +1,5 @@ +Metadata-Version: 2.1 +Name: itk +Version: @ITK_VER@ +Summary: Insight Segmentation and Registration Toolkit +Platform: UNKNOWN diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index a826cd6129c6..69513645108e 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -6206,6 +6206,12 @@ self: super: with self; { itanium-demangler = callPackage ../development/python-modules/itanium-demangler { }; + itk = toPythonModule (pkgs.itk.override { + inherit python numpy; + enablePython = true; + }); + + item-synchronizer = callPackage ../development/python-modules/item-synchronizer { }; itemadapter = callPackage ../development/python-modules/itemadapter { }; @@ -14477,7 +14483,7 @@ self: super: with self; { simplehound = callPackage ../development/python-modules/simplehound { }; simpleitk = callPackage ../development/python-modules/simpleitk { - inherit (pkgs) simpleitk; + inherit (pkgs) itk simpleitk; }; simplejson = callPackage ../development/python-modules/simplejson { };