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authorRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2019-08-15 09:26:55 +0200
committerRicardo Wurmus <rekado@elephly.net>2019-08-15 14:09:14 +0200
commit1c4e6aa9382e90acbf12246ce29357382902346d (patch)
tree8b54ae059dcba9987e3e70782b7e8c03e63aed5b /gnu/packages
parent07f36b0c53a644c11d26389de34e9d5e84469882 (diff)
downloadpatches-1c4e6aa9382e90acbf12246ce29357382902346d.tar
patches-1c4e6aa9382e90acbf12246ce29357382902346d.tar.gz
gnu: Add itk-snap.
* gnu/packages/image-processing.scm (itk-snap): New variable.
Diffstat (limited to 'gnu/packages')
-rw-r--r--gnu/packages/image-processing.scm139
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+)))