;;; Copyright © 2018 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
;;; Copyright © 2018 Lprndn <guix@lprndn.info>
;;; Copyright © 2019 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
#:use-module (gnu packages algebra)
#:use-module (gnu packages bison)
#:use-module (gnu packages boost)
+ #:use-module (gnu packages check)
#:use-module (gnu packages compression)
+ #:use-module (gnu packages curl)
#:use-module (gnu packages documentation)
#:use-module (gnu packages flex)
#:use-module (gnu packages fontutils)
#:use-module (gnu packages protobuf)
#:use-module (gnu packages python)
#:use-module (gnu packages python-xyz)
+ #:use-module (gnu packages qt)
#:use-module (gnu packages serialization)
+ #:use-module (gnu packages tbb)
#:use-module (gnu packages tls)
#:use-module (gnu packages video)
#:use-module (gnu packages xiph)
(define-public dcmtk
(package
(name "dcmtk")
- (version "3.6.4")
+ (version "3.6.5")
(source
(origin
(method url-fetch)
"dcmtk" (string-join (string-split version #\.) "")
"/dcmtk-" version ".tar.gz"))
(sha256
- (base32 "1h22z8g0kmvhg8lgkbikyzyphhvxvq6018a00yd6i4g0z9ag6gx9"))))
+ (base32 "1fdyz5wwjp4grys61mxb2ia9fi6i3ax6s43l16xnv291bxk7hld0"))))
(build-system cmake-build-system)
(inputs
`(;; Our ICU is too recent: “error: ‘UChar’ does not name a type“.
;; ("icu4c" ,icu4c)
- ("libjpeg" ,libjpeg)
+ ("libjpeg" ,libjpeg-turbo)
("libpng" ,libpng)
("libtiff" ,libtiff)
("libxml2" ,libxml2)
("gts" ,gts)
("hdf5" ,hdf5)
("itpp" ,itpp)
- ("libjpeg" ,libjpeg)
+ ("libjpeg" ,libjpeg-turbo)
("libpng" ,libpng)
("libtiff" ,libtiff)
("libxml" ,libxml2)
("expat" ,expat)
("freetype" ,freetype)
("hdf5" ,hdf5)
- ("jpeg" ,libjpeg)
+ ("jpeg" ,libjpeg-turbo)
("jsoncpp" ,jsoncpp)
("libogg" ,libogg)
("libtheora" ,libtheora)
(zero? (system (format #f "~a/bin/Xvfb ~a &" xorg-server disp)))))))))
(native-inputs
`(("pkg-config" ,pkg-config)
- ("xorg-server" ,xorg-server) ; For running the tests
+ ("xorg-server" ,xorg-server-for-tests) ; For running the tests
("opencv-extra"
,(origin
(method git-fetch)
(patches (search-patches "opencv-rgbd-aarch64-test-fix.patch"))
(sha256
(base32 "1f334glf39nk42mpqq6j732h3ql2mpz89jd4mcl678s8n73nfjh2"))))))
- (inputs `(("libjpeg" ,libjpeg)
+ (inputs `(("libjpeg" ,libjpeg-turbo)
("libpng" ,libpng)
("jasper" ,jasper)
;; ffmpeg 4.0 causes core dumps in tests.
("gobject-introspection" ,gobject-introspection)))
(inputs
`(("glib" ,glib)
- ("libjpeg" ,libjpeg)
+ ("libjpeg" ,libjpeg-turbo)
("libpng" ,libpng)
("librsvg" ,librsvg)
("libtiff" ,libtiff)
("gtk+-2" ,gtk+-2)
("libxml2" ,libxml2)
("libexif" ,libexif)
- ("libjpeg" ,libjpeg) ; required by vips.pc
+ ("libjpeg" ,libjpeg-turbo) ;required by vips.pc
("librsvg" ,librsvg)
("fftw" ,fftw)
("libgsf" ,libgsf)
(inputs
`(("libgeotiff" ,libgeotiff)
("libtiff" ,libtiff)
- ("libjpeg" ,libjpeg)
+ ("libjpeg" ,libjpeg-turbo)
("libpng" ,libpng)
("zlib" ,zlib)))
(home-page "https://github.com/vxl/vxl/")
`(#:configure-flags
;; Needed for itk-snap
(list "-DVNL_CONFIG_LEGACY_METHODS=ON")))))
+
+(define-public insight-toolkit
+ (package
+ (name "insight-toolkit")
+ (version "5.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/InsightSoftwareConsortium/ITK/"
+ "releases/download/v" version "/InsightToolkit-"
+ version ".tar.xz"))
+ (sha256
+ (base32 "0bs63mk4q8jmx38f031jy5w5n9yy5ng9x8ijwinvjyvas8cichqi"))))
+ (build-system cmake-build-system)
+ (arguments
+ `(#:tests? #f ; tests require network access and external data
+ #:configure-flags
+ '("-DITK_USE_GPU=ON"
+ "-DITK_USE_SYSTEM_LIBRARIES=ON"
+ "-DITK_USE_SYSTEM_GOOGLETEST=ON"
+ "-DITK_BUILD_SHARED=ON"
+ ;; This prevents "GTest::GTest" from being added to the ITK_LIBRARIES
+ ;; variable in the installed CMake files. This is necessary as other
+ ;; packages using insight-toolkit could not be configured otherwise.
+ "-DGTEST_ROOT=gtest")
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'do-not-tune
+ (lambda _
+ (substitute* "CMake/ITKSetStandardCompilerFlags.cmake"
+ (("-mute=native") ""))
+ #t)))))
+ (inputs
+ `(("eigen" ,eigen)
+ ("expat" ,expat)
+ ("fftw" ,fftw)
+ ("fftwf" ,fftwf)
+ ("hdf5" ,hdf5)
+ ("libjpeg" ,libjpeg-turbo)
+ ("libpng" ,libpng)
+ ("libtiff" ,libtiff)
+ ("mesa" ,mesa-opencl)
+ ("perl" ,perl)
+ ("python" ,python)
+ ("tbb" ,tbb)
+ ("vxl" ,vxl-1)
+ ("zlib" ,zlib)))
+ (native-inputs
+ `(("googletest" ,googletest)
+ ("pkg-config" ,pkg-config)))
+ (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
+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)))
+
+(define-public insight-toolkit-4
+ (package (inherit insight-toolkit)
+ (version "4.13.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/InsightSoftwareConsortium/ITK/"
+ "releases/download/v" version "/InsightToolkit-"
+ version ".tar.xz"))
+ (sha256
+ (base32 "19cgfpd63gqrvc3m27m394gy2d7w79g5y6lvznb5qqr49lihbgns"))))
+ (arguments
+ `(#:tests? #f ; tests require network access and external data
+ #:configure-flags
+ '("-DITKV3_COMPATIBILITY=ON" ; needed for itk-snap
+ "-DITK_USE_GPU=ON"
+ "-DITK_USE_SYSTEM_LIBRARIES=ON"
+ "-DITK_USE_SYSTEM_GOOGLETEST=ON"
+ "-DITK_USE_SYSTEM_VXL=ON")))))
+
+(define-public insight-toolkit-4.12
+ (package (inherit insight-toolkit-4)
+ (version "4.12.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://sourceforge/itk/itk/4.12/"
+ "InsightToolkit-" version ".tar.xz"))
+ (sha256
+ (base32 "1qw9mxbh083siljygahl4gdfv91xvfd8hfl7ghwii19f60xrvn2w"))))))
+
+(define-public itk-snap
+ (package
+ (name "itk-snap")
+ (version "3.8.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://git.code.sf.net/p/itk-snap/src")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "15i5ixpryfrbf3vrrb5rici8fb585f25k0v1ljds16bp1f1msr4q"))))
+ (build-system cmake-build-system)
+ (arguments
+ `(#:configure-flags
+ (list "-DSNAP_VERSION_GIT_SHA1=release"
+ "-DSNAP_VERSION_GIT_BRANCH=release"
+ "-DSNAP_VERSION_GIT_TIMESTAMP=0"
+ "-DSNAP_PACKAGE_QT_PLUGINS=OFF"
+ "-DCMAKE_POSITION_INDEPENDENT_CODE=ON")
+ #:phases
+ (modify-phases %standard-phases
+ ;; During the installation phase all libraries provided by all
+ ;; dependencies will be copied to the lib directory. That's insane,
+ ;; so we disable this.
+ (add-after 'unpack 'do-not-copy-dependencies
+ (lambda _
+ (substitute* "CMakeLists.txt"
+ (("install_qt5_executable\
+\\(\\$\\{SNAP_MAIN_INSTALL_DIR\\}/\\$\\{SNAP_EXE\\}\\)")
+ ""))
+ #t))
+ (add-after 'unpack 'disable-gui-tests
+ (lambda _
+ ;; The GUI tests just time out.
+ (substitute* "CMakeLists.txt"
+ ((" (Workspace|DiffSpace|ProbeIntensity|RegionCompetition\
+|RandomForest|RandomForestBailOut)")
+ ""))
+ #t))
+ (add-after 'unpack 'make-reproducible
+ (lambda _
+ (substitute* "CMakeLists.txt"
+ (("TODAY\\(SNAP_VERSION_COMPILE_DATE\\)")
+ "SET(SNAP_VERSION_COMPILE_DATE \"(removed for reproducibility)\")"))
+ #t))
+ (add-after 'unpack 'prepare-submodules
+ (lambda* (#:key inputs #:allow-other-keys)
+ (rmdir "Submodules/c3d")
+ (copy-recursively (assoc-ref inputs "c3d-src")
+ "Submodules/c3d")
+ (substitute* '("Submodules/c3d/adapters/BiasFieldCorrectionN4.cxx"
+ "Submodules/c3d/adapters/ApplyMetric.cxx")
+ (("vcl_") "std::"))
+ (rmdir "Submodules/greedy")
+ (symlink (assoc-ref inputs "greedy-src")
+ "Submodules/greedy")
+ #t))
+ (add-after 'unpack 'fix-includes
+ (lambda _
+ (substitute* "GUI/Model/RegistrationModel.cxx"
+ (("<vnl_symmetric_eigensystem.h>")
+ "<vnl/algo/vnl_symmetric_eigensystem.h>"))
+ #t))
+ (add-before 'check 'prepare-tests
+ (lambda _
+ ;; Needed by at least one test.
+ (setenv "HOME" "/tmp")
+ #t))
+ (add-after 'install 'wrap-executable
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (wrap-program (string-append out "/bin/itksnap")
+ `("QT_PLUGIN_PATH" ":" prefix
+ ,(map (lambda (label)
+ (string-append (assoc-ref inputs label)
+ "/lib/qt5/plugins"))
+ '("qtbase" "qtdeclarative"))))
+ #t))))))
+ (inputs
+ `(("curl" ,curl)
+ ("fftw" ,fftw)
+ ("fftwf" ,fftwf)
+ ("glu" ,glu)
+ ("hdf5" ,hdf5)
+ ("mesa" ,mesa-opencl)
+ ;; This package does not build with either insight-toolkit 5.0.0 and
+ ;; not with 4.13. It really needs to be 4.12.
+ ("itk" ,insight-toolkit-4.12)
+ ("vtk" ,vtk-6)
+ ("qtbase" ,qtbase)
+ ("qtdeclarative" ,qtdeclarative)
+ ("vxl" ,vxl-1)
+ ("zlib" ,zlib)))
+ (native-inputs
+ `(("googletest" ,googletest)
+ ("qttools" ,qttools)
+ ("pkg-config" ,pkg-config)
+ ("c3d-src"
+ ,(let* ((commit "f521358db26e00002c911cc47bf463b043942ad3")
+ (revision "1")
+ (version (git-version "0" revision commit)))
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/pyushkevich/c3d.git")
+ (commit commit)))
+ (file-name (git-file-name "c3d" version))
+ (sha256
+ (base32
+ "0kyv3rxrxwr8c3sa9zv01lsnhk95b27gx1s870k3yi8qp52h7bx3")))))
+ ;; We are using an arbitrary commit from 2017 because the latest
+ ;; version breaks the build...
+ ("greedy-src"
+ ,(let* ((commit "97e340f7e8e66597599144947775e6039e79a0d3")
+ (revision "1")
+ (version (git-version "0" revision commit)))
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/pyushkevich/greedy.git")
+ (commit commit)))
+ (file-name (git-file-name "greedy" version))
+ (sha256
+ (base32
+ "0k5bc9za4jrc8z9dj08z1rkcp5xf0gnd1d2jmi1w9ny4vxh2q2ab")))))))
+ (home-page "https://sourceforge.net/p/itk-snap/")
+ (synopsis "Medical image segmentation")
+ (description "ITK-SNAP is a tool for segmenting anatomical structures in
+medical images. It provides an automatic active contour segmentation
+pipeline, along with supporting a manual segmentation toolbox. ITK-SNAP has a
+full-featured UI aimed at clinical researchers.")
+ ;; This includes the submodules greedy and c3d.
+ (license license:gpl3+)))
HCoop / jackhill / guix / guix.git / blobdiff