@@ 88,6 88,7 @@
#:use-module (gnu packages image)
#:use-module (gnu packages imagemagick)
#:use-module (gnu packages linux)
+ #:use-module (gnu packages lua)
#:use-module (gnu packages maths)
#:use-module (gnu packages mpi)
#:use-module (gnu packages opencl)
@@ 108,6 109,7 @@
#:use-module (gnu packages sphinx)
#:use-module (gnu packages sqlite)
#:use-module (gnu packages ssh)
+ #:use-module (gnu packages statistics)
#:use-module (gnu packages swig)
#:use-module (gnu packages tbb)
#:use-module (gnu packages textutils)
@@ 1748,6 1750,122 @@ Scan Tailer Advanced is a fork of Scan Tailer that merges Scan Tailor Featured
and Scan Tailor Enhanced versions as well as including many more bug fixes.")
(license license:gpl3+))))
+(define-public simpleitk
+ (package
+ (name "simpleitk")
+ (version "2.5.2")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/SimpleITK/SimpleITK")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1ykrfrfh2012cg1122689w23pan2y731sszfpb701zhsb6fwv7j7"))))
+ (build-system cmake-build-system)
+ (outputs '("out" "python" "r"))
+ (arguments
+ (list
+ #:configure-flags
+ #~(list "-DBUILD_SHARED_LIBS=ON"
+ "-DWRAP_LUA=OFF"
+ "-DWRAP_PYTHON=ON"
+ "-DWRAP_R=ON"
+ "-DSimpleITK_PYTHON_USE_VIRTUALENV=OFF")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'early-GTest-discovery
+ (lambda _
+ ;; Find GTest before targets link to 'GTest::GTest'.
+ (substitute* "Testing/Unit/CMakeLists.txt"
+ (("add_subdirectory\\(TestBase\\)" anchor)
+ (string-append "find_package(GTest REQUIRED)\n" anchor)))))
+ (add-after 'unpack 'extract-test-data
+ (lambda _
+ (invoke "tar" "xvf"
+ #$(this-package-native-input
+ (string-append "SimpleITKData-" version ".tar.gz"))
+ "--strip-components=1")))
+ (add-after 'unpack 'fix-runpath
+ (lambda _
+ ;; The SWIG-generated shared libraries do not have SimpleITK's
+ ;; libraries in their RUNPATH.
+ (define (cmake-snippet start)
+ (string-append
+ start
+ "set_target_properties(${SWIG_MODULE_SimpleITK_TARGET_NAME} "
+ "PROPERTIES BUILD_WITH_INSTALL_RPATH TRUE "
+ "INSTALL_RPATH \"" #$output "/lib\")\n"))
+ (substitute* "Wrapping/Python/CMakeLists.txt"
+ (("^set\\(SWIG_MODULE_SimpleITKPython.*" anchor)
+ (cmake-snippet anchor)))
+ (substitute* "Wrapping/R/CMakeLists.txt"
+ (("^set\\(SWIG_MODULE_SimpleITKR.*" anchor)
+ (cmake-snippet anchor)))))
+ (add-after 'unpack 'patch-cmake-config-itk-path
+ (lambda _
+ ;; Allow building SimpleITK C++ projects without ITK installed
+ ;; in the profile.
+ #$(let*
+ ((itk (this-package-input "insight-toolkit"))
+ (itk-version (package-version itk))
+ (itk-version-major+minor
+ (version-major+minor itk-version)))
+ #~(substitute* "SimpleITKConfig.cmake.in"
+ (((string-append
+ "find_package\\(ITK \"@ITK_VERSION@\" "
+ "EXACT REQUIRED\\)"))
+ (string-append
+ "find_package(ITK \"" #$itk-version
+ "\" EXACT REQUIRED PATHS " #$itk
+ "/lib/cmake/ITK-"
+ #$itk-version-major+minor ")"))))))
+ (add-after 'install 'install-language-extension-modules
+ (lambda _
+ (with-directory-excursion "Wrapping/Python"
+ (invoke "python3" "setup.py" "bdist_wheel")
+ (apply invoke "pip" "--no-cache-dir" "--no-input" "install"
+ "--no-deps" "--prefix" #$output:python
+ (find-files "dist" "\\.whl$")))
+ (let ((r-package-path
+ (string-append #$output:r "/site-library/SimpleITK")))
+ (mkdir-p r-package-path)
+ (copy-recursively "Wrapping/R/R_libs/SimpleITK"
+ r-package-path))))
+ (delete 'check)
+ (add-after 'install 'check-after-install
+ ;; Run the tests when the SimpleITK libraries are where the
+ ;; language extension modules expect them to be.
+ (assoc-ref %standard-phases 'check)))))
+ (home-page "https://simpleitk.org")
+ (inputs (list insight-toolkit python r-minimal))
+ (native-inputs
+ (list googletest
+ lua
+ python-numpy ;for tests
+ python-pip
+ python-setuptools
+ python-wheel
+ swig-next
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/SimpleITK/SimpleITK/releases/download/v"
+ version "/SimpleITKData-" version ".tar.gz"))
+ (sha256
+ (base32
+ "13y44qqsgsvbrm84073i8clhggdgk8f36i6102sjg4j3fq790gal")))))
+ (synopsis "Simplified interface to @acronym{ITK, Insight Toolkit}")
+ (description
+ "SimpleITK is an image analysis toolkit built on top of @acronym{ITK,
+Insight Toolkit}. It provides a simplified interface to most of the
+image filters and the input/output and registration frameworks in
+@acronym{ITK, Insight Toolkit}. It is written in C++ and provides
+bindings for interpreted languages. This package includes the C++,
+Python and R interfaces.")
+ (license license:asl2.0)))
+
(define-public stiff
(package
(name "stiff")