guix_mirror_bot pushed a commit to branch master
in repository guix.
commit 61a1741f3888a8ab3f698c4ed0973789c66c8914
Author: Jake Forster <[email protected]>
AuthorDate: Sat Jul 26 00:46:45 2025 +0930
gnu: insight-toolkit: Include remote module for ITK-SNAP.
* gnu/packages/image-processing.scm (insight-toolkit)[arguments]
<#:configure-flags>: Add "-DModule_MorphologicalContourInterpolation=ON".
<#:phases>: Add phase 'prepare-remote-modules.
[native-inputs]: Add origin for MorphologicalContourInterpolation checkout.
Change-Id: I441f250d42f5ac1077c72a3c15281dd327264f3b
Co-authored-by: Andreas Enge <[email protected]>
Signed-off-by: Andreas Enge <[email protected]>
---
gnu/packages/image-processing.scm | 239 ++++++++++++++++++++++----------------
1 file changed, 141 insertions(+), 98 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 <[email protected]>
;;; Copyright © 2025 Jake Forster <[email protected]>
;;; Copyright © 2025 Anderson Torres <[email protected]>
+;;; Copyright © 2025 Andreas Enge <[email protected]>
;;;
;;; 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")
-
- #: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))
-
- ;; 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)))
+ ;; 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")
- (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
+ #: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)))
+
+ (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)
