diff options
| -rw-r--r-- | gnu/packages/image-processing.scm | 235 |
1 files changed, 139 insertions, 96 deletions
diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-processing.scm index c6c20c690b..6c8dc1b8c5 100644 --- a/gnu/packages/image-processing.scm +++ b/gnu/packages/image-processing.scm @@ -26,6 +26,7 @@ ;;; Copyright © 2024 Nicolas Graves <ngraves@ngraves.fr> ;;; Copyright © 2025 Jake Forster <jakecameron.forster@gmail.com> ;;; Copyright © 2025 Anderson Torres <anderson.torres.8519@gmail.com> +;;; Copyright © 2025 Andreas Enge <andreas@enge.fr> ;;; ;;; This file is part of GNU Guix. ;;; @@ -1256,104 +1257,146 @@ libraries designed for computer vision research and implementation.") "-DCMAKE_CXX_STANDARD=14"))))) (define-public insight-toolkit - (package - (name "insight-toolkit") - (version "5.4.4") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/InsightSoftwareConsortium/ITK") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "1l5rby8jj8726k380aivycmhn56cz56mr9k3r56c8hkkrfwwng50")) - ;; This patch is required to build with both ITK_USE_GPU=ON and - ;; ITK_WRAP_PYTHON=ON. - ;; <https://github.com/InsightSoftwareConsortium/ITK/pull/4842> - (patches (search-patches "insight-toolkit-fix-build.patch")))) - (build-system cmake-build-system) - (outputs '("out" "python")) - (arguments - (list #:tests? #f ; tests require network access and external data - #:configure-flags - #~(list "-DITK_USE_GPU=ON" - "-DITK_USE_SYSTEM_LIBRARIES=ON" - "-DITK_USE_SYSTEM_CASTXML=ON" - "-DITK_USE_SYSTEM_SWIG=ON" - (string-append "-DHDF5_DIR=" #$(this-package-input "hdf5") - "/lib/cmake") - "-DBUILD_SHARED_LIBS=ON" - ;; Without this flag, there are shared libraries installed - ;; in PY_SITE_PACKAGES_PATH/itk instead of #$output/lib and - ;; RUNPATHs contain the *build directory* of - ;; PY_SITE_PACKAGES_PATH/itk. - "-DCMAKE_BUILD_WITH_INSTALL_RPATH=ON" - "-DITK_WRAPPING=ON" - "-DITK_WRAP_PYTHON=ON" - "-DITK_DYNAMIC_LOADING=ON" - (let* ((python-version - #$(version-major+minor - (package-version (this-package-input "python")))) - (python-lib-path - (string-append #$output:python - "/lib/python" python-version - "/site-packages"))) - (string-append "-DPY_SITE_PACKAGES_PATH=" python-lib-path)) - ;; Python is not built with Py_LIMITED_API. - "-DITK_USE_PYTHON_LIMITED_API=OFF" - "-DCMAKE_CXX_STANDARD=17" - "-DBUILD_TESTING=OFF") + ;; For information about ITK remote modules, see: + ;; https://insightsoftwareconsortium.github.io/ITKWikiArchive/Wiki/ITK/Policy_and_Procedures_for_Adding_Remote_Modules + ;; For a remote MODULE, use the commit in + ;; 'Modules/Remote/MODULE.remote.cmake'. + ;; MorphologicalContourInterpolation is required by itk-snap. + (let* ((module-commit "821bf9b3ef8eaaab10391ed060dc9ca5e4d37b39") + (module-file (git-file-name "ITKMorphologicalContourInterpolation" + module-commit))) + (package + (name "insight-toolkit") + (version "5.4.4") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/InsightSoftwareConsortium/ITK") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1l5rby8jj8726k380aivycmhn56cz56mr9k3r56c8hkkrfwwng50")) + ;; This patch is required to build with both ITK_USE_GPU=ON and + ;; ITK_WRAP_PYTHON=ON. + ;; <https://github.com/InsightSoftwareConsortium/ITK/pull/4842> + (patches (search-patches "insight-toolkit-fix-build.patch")))) + (build-system cmake-build-system) + (outputs '("out" "python")) + (arguments + (list + #:tests? #f ;tests require network access and external data + #:configure-flags + #~(list "-DITK_USE_GPU=ON" + "-DITK_USE_SYSTEM_LIBRARIES=ON" + "-DITK_USE_SYSTEM_CASTXML=ON" + "-DITK_USE_SYSTEM_SWIG=ON" + (string-append "-DHDF5_DIR=" + #$(this-package-input "hdf5") "/lib/cmake") + "-DBUILD_SHARED_LIBS=ON" + ;; Without this flag, there are shared libraries installed + ;; in PY_SITE_PACKAGES_PATH/itk instead of #$output/lib and + ;; RUNPATHs contain the *build directory* of + ;; PY_SITE_PACKAGES_PATH/itk. + "-DCMAKE_BUILD_WITH_INSTALL_RPATH=ON" + "-DITK_WRAPPING=ON" + "-DITK_WRAP_PYTHON=ON" + "-DITK_DYNAMIC_LOADING=ON" + (let* ((python-version + #$(version-major+minor + (package-version + (this-package-input "python")))) + (python-lib-path (string-append #$output:python + "/lib/python" + python-version + "/site-packages"))) + (string-append "-DPY_SITE_PACKAGES_PATH=" + python-lib-path)) + ;; Python is not built with Py_LIMITED_API. + "-DITK_USE_PYTHON_LIMITED_API=OFF" + "-DModule_MorphologicalContourInterpolation=ON" + "-DCMAKE_CXX_STANDARD=17" + "-DBUILD_TESTING=OFF") - #:phases #~(modify-phases %standard-phases - (add-after 'unpack 'do-not-tune - (lambda _ - (substitute* "CMake/ITKSetStandardCompilerFlags.cmake" - (("-mtune=native") - "")))) - (add-after 'unpack 'ignore-warnings - (lambda _ - (substitute* "Wrapping/Generators/Python/CMakeLists.txt" - (("-Werror") "")))) - (add-after 'unpack 'exclude-gtest-target - (lambda _ - ;; Prevent ITKGoogleTest from being added to - ;; ITK_MODULES_ENABLED in the installed - ;; ITKConfig.cmake, which in turn prevents - ;; 'GTest::GTest' from being added to the - ;; ITK_LIBRARIES variable. This is necessary - ;; because projects that use ITK fail to configure - ;; otherwise. Fixes - ;; <https://codeberg.org/guix/guix/issues/776>. - ;; <https://github.com/microsoft/vcpkg/pull/27187> - (substitute* "Modules/ThirdParty/GoogleTest/itk-module.cmake" - (("DEPENDS") "DEPENDS\n EXCLUDE_FROM_DEFAULT"))))))) - (inputs - (list eigen - expat - fftw - fftwf - hdf5 - libjpeg-turbo - libpng - libtiff - mesa-opencl - perl - python - tbb - vxl-1 - zlib)) - (native-inputs - (list castxml gcc-13 git-minimal pkg-config swig-next which)) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'do-not-tune + (lambda _ + (substitute* "CMake/ITKSetStandardCompilerFlags.cmake" + (("-mtune=native") + "")))) + (add-after 'unpack 'ignore-warnings + (lambda _ + (substitute* "Wrapping/Generators/Python/CMakeLists.txt" + (("-Werror") + "")))) + (add-after 'unpack 'exclude-gtest-target + (lambda _ + ;; Prevent ITKGoogleTest from being added to + ;; ITK_MODULES_ENABLED in the installed + ;; ITKConfig.cmake, which in turn prevents + ;; 'GTest::GTest' from being added to the + ;; ITK_LIBRARIES variable. This is necessary + ;; because projects that use ITK fail to configure + ;; otherwise. Fixes + ;; <https://codeberg.org/guix/guix/issues/776>. + ;; <https://github.com/microsoft/vcpkg/pull/27187> + (substitute* "Modules/ThirdParty/GoogleTest/itk-module.cmake" + (("DEPENDS") + "DEPENDS\n EXCLUDE_FROM_DEFAULT")))) + (add-after 'unpack 'prepare-remote-modules + (lambda _ + ;; ITK module MorphologicalContourInterpolation + ;; is for ITK-SNAP. + (symlink #$(this-package-native-input module-file) + "Modules/Remote/MorphologicalContourInterpolation") + (delete-file + (string-append + "Modules/Remote/" + "MorphologicalContourInterpolation.remote.cmake"))))))) + (inputs (list eigen + expat + fftw + fftwf + hdf5 + libjpeg-turbo + libpng + libtiff + mesa-opencl + perl + python + tbb + vxl-1 + zlib)) + (native-inputs + (list castxml + gcc-13 + git-minimal + pkg-config + swig-next + which + (origin + (method git-fetch) + (uri + (git-reference + (url (string-append + "https://github.com/KitwareMedical/" + "ITKMorphologicalContourInterpolation")) + (commit module-commit))) + (file-name module-file) + (sha256 + (base32 + "00myhgvlk3n062i8bnknz1d10zkv3jlvs7f4jnk24727gd4v2n4i"))))) - ;; The 'CMake/ITKSetStandardCompilerFlags.cmake' file normally sets - ;; '-mtune=native -march=corei7', suggesting there's something to be - ;; gained from CPU-specific optimizations. - (properties '((tunable? . #t))) + ;; The 'CMake/ITKSetStandardCompilerFlags.cmake' file normally sets + ;; '-mtune=native -march=corei7', suggesting there's something to be + ;; gained from CPU-specific optimizations. + (properties '((tunable? . #t))) - (home-page "https://github.com/InsightSoftwareConsortium/ITK/") - (synopsis "Scientific image processing, segmentation and registration") - (description "The Insight Toolkit (ITK) is a toolkit for N-dimensional + (home-page "https://github.com/InsightSoftwareConsortium/ITK/") + (synopsis "Scientific image processing, segmentation and registration") + (description + "The Insight Toolkit (ITK) is a toolkit for N-dimensional scientific image processing, segmentation, and registration. Segmentation is the process of identifying and classifying data found in a digitally sampled representation. Typically the sampled representation is an image acquired @@ -1361,7 +1404,7 @@ from such medical instrumentation as CT or MRI scanners. Registration is the task of aligning or developing correspondences between data. For example, in the medical environment, a CT scan may be aligned with a MRI scan in order to combine the information contained in both.") - (license license:asl2.0))) + (license license:asl2.0)))) (define-public insight-toolkit-4 (package (inherit insight-toolkit) |