diff options
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/image-processing.scm | 139 |
1 files changed, 139 insertions, 0 deletions
diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-processing.scm index 3fa1be4244..b3972a2b76 100644 --- a/gnu/packages/image-processing.scm +++ b/gnu/packages/image-processing.scm @@ -38,6 +38,7 @@ #: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) @@ -60,6 +61,7 @@ #: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) @@ -702,3 +704,140 @@ combine the information contained in both.") "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" + "-DCMAKE_CXX_FLAGS=-std=gnu++11 -fpermissive") + #: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) + ("qttools" ,qttools) + ("vxl" ,vxl-1) + ("zlib" ,zlib))) + (native-inputs + `(("googletest" ,googletest) + ("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+))) |