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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 <andreas@enge.fr> Signed-off-by: Andreas Enge <andreas@enge.fr>
This commit is contained in:
Jake Forster
Andreas Enge
parent
2b7aefcf2c
commit
61a1741f38
1 changed files with 139 additions and 96 deletions
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@ -26,6 +26,7 @@
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;;; Copyright © 2024 Nicolas Graves <ngraves@ngraves.fr>
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;;; Copyright © 2025 Jake Forster <jakecameron.forster@gmail.com>
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;;; Copyright © 2025 Anderson Torres <anderson.torres.8519@gmail.com>
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;;; Copyright © 2025 Andreas Enge <andreas@enge.fr>
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;;;
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;;; This file is part of GNU Guix.
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;;;
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@ -1256,104 +1257,146 @@ libraries designed for computer vision research and implementation.")
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"-DCMAKE_CXX_STANDARD=14")))))
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(define-public insight-toolkit
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(package
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(name "insight-toolkit")
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(version "5.4.4")
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/InsightSoftwareConsortium/ITK")
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(commit (string-append "v" version))))
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(file-name (git-file-name name version))
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(sha256
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(base32 "1l5rby8jj8726k380aivycmhn56cz56mr9k3r56c8hkkrfwwng50"))
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;; This patch is required to build with both ITK_USE_GPU=ON and
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;; ITK_WRAP_PYTHON=ON.
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;; <https://github.com/InsightSoftwareConsortium/ITK/pull/4842>
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(patches (search-patches "insight-toolkit-fix-build.patch"))))
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(build-system cmake-build-system)
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(outputs '("out" "python"))
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(arguments
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(list #:tests? #f ; tests require network access and external data
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#:configure-flags
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#~(list "-DITK_USE_GPU=ON"
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"-DITK_USE_SYSTEM_LIBRARIES=ON"
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"-DITK_USE_SYSTEM_CASTXML=ON"
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"-DITK_USE_SYSTEM_SWIG=ON"
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(string-append "-DHDF5_DIR=" #$(this-package-input "hdf5")
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"/lib/cmake")
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"-DBUILD_SHARED_LIBS=ON"
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;; Without this flag, there are shared libraries installed
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;; in PY_SITE_PACKAGES_PATH/itk instead of #$output/lib and
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;; RUNPATHs contain the *build directory* of
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;; PY_SITE_PACKAGES_PATH/itk.
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"-DCMAKE_BUILD_WITH_INSTALL_RPATH=ON"
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"-DITK_WRAPPING=ON"
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"-DITK_WRAP_PYTHON=ON"
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"-DITK_DYNAMIC_LOADING=ON"
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(let* ((python-version
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#$(version-major+minor
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(package-version (this-package-input "python"))))
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(python-lib-path
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(string-append #$output:python
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"/lib/python" python-version
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"/site-packages")))
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(string-append "-DPY_SITE_PACKAGES_PATH=" python-lib-path))
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;; Python is not built with Py_LIMITED_API.
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"-DITK_USE_PYTHON_LIMITED_API=OFF"
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"-DCMAKE_CXX_STANDARD=17"
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"-DBUILD_TESTING=OFF")
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;; For information about ITK remote modules, see:
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;; https://insightsoftwareconsortium.github.io/ITKWikiArchive/Wiki/ITK/Policy_and_Procedures_for_Adding_Remote_Modules
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;; For a remote MODULE, use the commit in
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;; 'Modules/Remote/MODULE.remote.cmake'.
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;; MorphologicalContourInterpolation is required by itk-snap.
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(let* ((module-commit "821bf9b3ef8eaaab10391ed060dc9ca5e4d37b39")
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(module-file (git-file-name "ITKMorphologicalContourInterpolation"
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module-commit)))
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(package
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(name "insight-toolkit")
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(version "5.4.4")
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/InsightSoftwareConsortium/ITK")
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(commit (string-append "v" version))))
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(file-name (git-file-name name version))
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(sha256
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(base32 "1l5rby8jj8726k380aivycmhn56cz56mr9k3r56c8hkkrfwwng50"))
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;; This patch is required to build with both ITK_USE_GPU=ON and
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;; ITK_WRAP_PYTHON=ON.
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;; <https://github.com/InsightSoftwareConsortium/ITK/pull/4842>
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(patches (search-patches "insight-toolkit-fix-build.patch"))))
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(build-system cmake-build-system)
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(outputs '("out" "python"))
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(arguments
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(list
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#:tests? #f ;tests require network access and external data
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#:configure-flags
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#~(list "-DITK_USE_GPU=ON"
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"-DITK_USE_SYSTEM_LIBRARIES=ON"
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"-DITK_USE_SYSTEM_CASTXML=ON"
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"-DITK_USE_SYSTEM_SWIG=ON"
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(string-append "-DHDF5_DIR="
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#$(this-package-input "hdf5") "/lib/cmake")
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"-DBUILD_SHARED_LIBS=ON"
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;; Without this flag, there are shared libraries installed
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;; in PY_SITE_PACKAGES_PATH/itk instead of #$output/lib and
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;; RUNPATHs contain the *build directory* of
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;; PY_SITE_PACKAGES_PATH/itk.
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"-DCMAKE_BUILD_WITH_INSTALL_RPATH=ON"
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"-DITK_WRAPPING=ON"
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"-DITK_WRAP_PYTHON=ON"
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"-DITK_DYNAMIC_LOADING=ON"
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(let* ((python-version
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#$(version-major+minor
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(package-version
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(this-package-input "python"))))
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(python-lib-path (string-append #$output:python
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"/lib/python"
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python-version
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"/site-packages")))
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(string-append "-DPY_SITE_PACKAGES_PATH="
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python-lib-path))
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;; Python is not built with Py_LIMITED_API.
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"-DITK_USE_PYTHON_LIMITED_API=OFF"
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"-DModule_MorphologicalContourInterpolation=ON"
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"-DCMAKE_CXX_STANDARD=17"
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"-DBUILD_TESTING=OFF")
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#:phases #~(modify-phases %standard-phases
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(add-after 'unpack 'do-not-tune
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(lambda _
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(substitute* "CMake/ITKSetStandardCompilerFlags.cmake"
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(("-mtune=native")
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""))))
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(add-after 'unpack 'ignore-warnings
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(lambda _
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(substitute* "Wrapping/Generators/Python/CMakeLists.txt"
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(("-Werror") ""))))
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(add-after 'unpack 'exclude-gtest-target
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(lambda _
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;; Prevent ITKGoogleTest from being added to
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;; ITK_MODULES_ENABLED in the installed
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;; ITKConfig.cmake, which in turn prevents
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;; 'GTest::GTest' from being added to the
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;; ITK_LIBRARIES variable. This is necessary
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;; because projects that use ITK fail to configure
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;; otherwise. Fixes
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;; <https://codeberg.org/guix/guix/issues/776>.
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;; <https://github.com/microsoft/vcpkg/pull/27187>
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(substitute* "Modules/ThirdParty/GoogleTest/itk-module.cmake"
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(("DEPENDS") "DEPENDS\n EXCLUDE_FROM_DEFAULT")))))))
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(inputs
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(list eigen
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expat
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fftw
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fftwf
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hdf5
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libjpeg-turbo
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libpng
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libtiff
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mesa-opencl
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perl
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python
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tbb
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vxl-1
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zlib))
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(native-inputs
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(list castxml gcc-13 git-minimal pkg-config swig-next which))
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#:phases
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#~(modify-phases %standard-phases
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(add-after 'unpack 'do-not-tune
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(lambda _
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(substitute* "CMake/ITKSetStandardCompilerFlags.cmake"
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(("-mtune=native")
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""))))
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(add-after 'unpack 'ignore-warnings
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(lambda _
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(substitute* "Wrapping/Generators/Python/CMakeLists.txt"
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(("-Werror")
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""))))
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(add-after 'unpack 'exclude-gtest-target
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(lambda _
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;; Prevent ITKGoogleTest from being added to
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;; ITK_MODULES_ENABLED in the installed
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;; ITKConfig.cmake, which in turn prevents
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;; 'GTest::GTest' from being added to the
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;; ITK_LIBRARIES variable. This is necessary
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;; because projects that use ITK fail to configure
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;; otherwise. Fixes
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;; <https://codeberg.org/guix/guix/issues/776>.
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;; <https://github.com/microsoft/vcpkg/pull/27187>
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(substitute* "Modules/ThirdParty/GoogleTest/itk-module.cmake"
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(("DEPENDS")
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"DEPENDS\n EXCLUDE_FROM_DEFAULT"))))
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(add-after 'unpack 'prepare-remote-modules
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(lambda _
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;; ITK module MorphologicalContourInterpolation
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;; is for ITK-SNAP.
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(symlink #$(this-package-native-input module-file)
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"Modules/Remote/MorphologicalContourInterpolation")
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(delete-file
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(string-append
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"Modules/Remote/"
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"MorphologicalContourInterpolation.remote.cmake")))))))
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(inputs (list eigen
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expat
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fftw
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fftwf
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hdf5
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libjpeg-turbo
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libpng
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libtiff
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mesa-opencl
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perl
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python
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tbb
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vxl-1
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zlib))
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(native-inputs
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(list castxml
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gcc-13
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git-minimal
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pkg-config
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swig-next
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which
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(origin
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(method git-fetch)
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(uri
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(git-reference
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(url (string-append
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"https://github.com/KitwareMedical/"
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"ITKMorphologicalContourInterpolation"))
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(commit module-commit)))
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(file-name module-file)
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(sha256
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(base32
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"00myhgvlk3n062i8bnknz1d10zkv3jlvs7f4jnk24727gd4v2n4i")))))
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;; The 'CMake/ITKSetStandardCompilerFlags.cmake' file normally sets
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;; '-mtune=native -march=corei7', suggesting there's something to be
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;; gained from CPU-specific optimizations.
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(properties '((tunable? . #t)))
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;; The 'CMake/ITKSetStandardCompilerFlags.cmake' file normally sets
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;; '-mtune=native -march=corei7', suggesting there's something to be
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;; gained from CPU-specific optimizations.
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(properties '((tunable? . #t)))
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(home-page "https://github.com/InsightSoftwareConsortium/ITK/")
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(synopsis "Scientific image processing, segmentation and registration")
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(description "The Insight Toolkit (ITK) is a toolkit for N-dimensional
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(home-page "https://github.com/InsightSoftwareConsortium/ITK/")
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(synopsis "Scientific image processing, segmentation and registration")
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(description
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"The Insight Toolkit (ITK) is a toolkit for N-dimensional
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scientific image processing, segmentation, and registration. Segmentation is
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the process of identifying and classifying data found in a digitally sampled
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representation. Typically the sampled representation is an image acquired
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@ -1361,7 +1404,7 @@ from such medical instrumentation as CT or MRI scanners. Registration is the
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task of aligning or developing correspondences between data. For example, in
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the medical environment, a CT scan may be aligned with a MRI scan in order to
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combine the information contained in both.")
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(license license:asl2.0)))
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(license license:asl2.0))))
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(define-public insight-toolkit-4
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(package (inherit insight-toolkit)
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