;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2017 John Darrington <jmd@gnu.org>
-;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2017, 2019 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2014 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2014 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.org>
-;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
;;; Copyright © 2018 Lprndn <guix@lprndn.info>
;;; Copyright © 2019 Efraim Flashner <efraim@flashner.co.il>
#:use-module (guix packages)
#:use-module (guix utils)
#:use-module (guix download)
+ #:use-module (guix git-download)
#:use-module (guix build-system cmake)
#:use-module (guix build-system gnu)
#:use-module (gnu packages)
#: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 geo)
#:use-module (gnu packages ghostscript)
#:use-module (gnu packages gl)
#:use-module (gnu packages glib)
#:use-module (gnu packages pkg-config)
#: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)
#:use-module (gnu packages xml)
- #:use-module (gnu packages xorg))
+ #:use-module (gnu packages xorg)
+ #:use-module (ice-9 match)
+ #:use-module (srfi srfi-1))
-;; We use the latest snapshot of this package because the latest release is
-;; from 2011 and has known vulnerabilities that cannot easily be fixed by
-;; applying patches.
(define-public dcmtk
(package
(name "dcmtk")
- (version "3.6.1_20170228")
- (source (origin
- (method url-fetch)
- (uri (string-append "ftp://dicom.offis.de/pub/dicom/offis/"
- "software/dcmtk/snapshot/dcmtk-"
- version ".tar.gz"))
- (sha256
- (base32
- "04cwfx8yrscqcd59mxk2fh6314ckayi9cp68iql5a57pf2pg5qld"))))
- (build-system gnu-build-system)
+ (version "3.6.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri
+ (string-append "ftp://dicom.offis.de/pub/dicom/offis/software/dcmtk/"
+ "dcmtk" (string-join (string-split version #\.) "")
+ "/dcmtk-" version ".tar.gz"))
+ (sha256
+ (base32 "1fdyz5wwjp4grys61mxb2ia9fi6i3ax6s43l16xnv291bxk7hld0"))))
+ (build-system cmake-build-system)
(inputs
- `(("libtiff" ,libtiff)
+ `(;; Our ICU is too recent: “error: ‘UChar’ does not name a type“.
+ ;; ("icu4c" ,icu4c)
+ ("libjpeg" ,libjpeg)
("libpng" ,libpng)
- ("doxygen" ,doxygen)
+ ("libtiff" ,libtiff)
+ ("libxml2" ,libxml2)
+ ("openssl" ,openssl)
("zlib" ,zlib)))
(native-inputs
- `(("perl" ,perl)))
- (home-page "http://dcmtk.org")
+ `(("doxygen" ,doxygen))) ; for HTML documentation
+ (home-page "https://dcmtk.org")
(synopsis "Libraries and programs implementing parts of the DICOM standard")
(description "DCMTK is a collection of libraries and applications
implementing large parts the DICOM standard. It includes software for
(define-public vtk
(package
(name "vtk")
- (version "7.1.0")
+ (version "8.2.0")
(source (origin
(method url-fetch)
- (uri (string-append "http://www.vtk.org/files/release/"
+ (uri (string-append "https://vtk.org/files/release/"
(version-major+minor version)
"/VTK-" version ".tar.gz"))
(sha256
(base32
- "0yj96z58haan77gzilnqp7xpf8hg5jk11a3jx55p2ksd400s0gjz"))))
+ "1fspgp8k0myr6p2a6wkc21ldcswb4bvmb484m12mxgk1a9vxrhrl"))))
(build-system cmake-build-system)
(arguments
'(#:build-type "Release" ;Build without '-g' to save space.
("png" ,libpng)
("tiff" ,libtiff)
("zlib" ,zlib)))
- (home-page "http://www.vtk.org/")
+ (home-page "https://vtk.org/")
(synopsis "Libraries for 3D computer graphics")
(description
"The Visualization Toolkit (VTK) is a C++ library for 3D computer graphics,
integrates with various databases on GUI toolkits such as Qt and Tk.")
(license license:bsd-3)))
+;; itksnap needs an older variant of VTK.
+(define-public vtk-6
+ (package (inherit vtk)
+ (version "6.3.0")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://vtk.org/files/release/"
+ (version-major+minor version)
+ "/VTK-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0pla1r5mvkgl4sl213gfdhzrypdgai0h3z5mfgm6p9jz9hsr794j"))))
+ (inputs
+ `(("jsoncpp" ,jsoncpp-for-tensorflow)
+ ,@(alist-delete "jsoncpp" (package-inputs vtk))))))
+
(define-public opencv
(package
(name "opencv")
(version "3.4.3")
(source (origin
- (method url-fetch)
- (uri (string-append "https://github.com/opencv/opencv/archive/"
- version ".zip"))
- (file-name (string-append name "-" version ".zip"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/opencv/opencv")
+ (commit version)))
+ (file-name (git-file-name name version))
(sha256
(base32
- "0pycx1pz8lj794q32mlalyc3ijqxwsyin65r26nh4yc0p71xiirp"))
+ "06bc61r8myym4s8im10brdjfg4wxkrvsbhhl7vr1msdan2xddzi3"))
(modules '((guix build utils)))
(snippet
'(begin
;; Some jars found:
(for-each delete-file
'("modules/java/test/pure_test/lib/junit-4.11.jar"
- "samples/java/sbt/sbt/sbt-launch.jar"))))))
+ "samples/java/sbt/sbt/sbt-launch.jar"))
+ #t))))
(build-system cmake-build-system)
(arguments
`(#:configure-flags
;; (CPU_ALL_OPTIMIZATIONS) for a list of all optimizations
;; BASELINE is the minimum optimization all CPUs must support
;;
- ;; DISPATCH is the list of optional dispatches. We add them all.
- "-DCPU_BASELINE=SSE2, NEON"
+ ;; DISPATCH is the list of optional dispatches.
+ "-DCPU_BASELINE=SSE2"
- "-DCPU_DISPATCH=NEON;VFPV3;FP16;SSE;SSE2;SSE3;SSSE3;SSE4_1;SSE4_2;POPCNT;AVX;FP16;AVX2;FMA3;AVX_512F;AVX512_SKX"
- ,@(if (string-prefix? "x86_64" (or (%current-target-system)
- (%current-system)))
- '("-DCPU_DISPATCH_REQUIRE=SSE3,SSSE3,SSE4_1,SSE4_2,AVX,AVX2")
- '())
+ ,@(match (%current-system)
+ ("x86_64-linux"
+ '("-DCPU_DISPATCH=NEON;VFPV3;FP16;SSE;SSE2;SSE3;SSSE3;SSE4_1;SSE4_2;POPCNT;AVX;FP16;AVX2;FMA3;AVX_512F;AVX512_SKX"
+ "-DCPU_DISPATCH_REQUIRE=SSE3,SSSE3,SSE4_1,SSE4_2,AVX,AVX2"))
+ ("armhf-linux"
+ '("-DCPU_BASELINE_DISABLE=NEON")) ; causes build failures
+ ("aarch64-linux"
+ '("-DCPU_BASELINE=NEON"
+ "-DCPU_DISPATCH=NEON;VFPV3;FP16"))
+ (_ '()))
"-DBUILD_PERF_TESTS=OFF"
"-DBUILD_TESTS=ON"
(string-append "-DOPENCV_EXTRA_MODULES_PATH=" (getcwd)
- "/opencv-contrib/opencv_contrib-" ,version
- "/modules")
+ "/opencv-contrib/modules")
;;Define test data:
(string-append "-DOPENCV_TEST_DATA_PATH=" (getcwd)
- "/opencv-extra/opencv_extra-" ,version
- "/testdata")
+ "/opencv-extra/testdata")
;; Is ON by default and would try to rebuild 3rd-party protobuf,
;; which we had removed, which would lead to an error:
;; This one fails with "unknown file: Failure"
;; But I couldn't figure out which file was missing:
- (substitute* (list (string-append
- "../opencv-contrib/opencv_contrib-"
- ,version
- "/modules/face/test/test_face_align.cpp"))
+ (substitute* "../opencv-contrib/modules/face/test/test_face_align.cpp"
(("(TEST\\(CV_Face_FacemarkKazemi, )(can_detect_landmarks\\).*)"
all pre post)
(string-append pre "DISABLED_" post)))
;; Failure reason: Bad accuracy
;; Incorrect count of accurate poses [2nd case]: 90.000000 / 94.000000
- (substitute* (list (string-append
- "../opencv-contrib/opencv_contrib-"
- ,version
- "/modules/rgbd/test/test_odometry.cpp"))
+ (substitute* "../opencv-contrib/modules/rgbd/test/test_odometry.cpp"
(("(TEST\\(RGBD_Odometry_Rgbd, )(algorithmic\\).*)" all pre post)
(string-append pre "DISABLED_" post)))
#t))
- ;; Idea copied from ldc.scm (ldc-bootstrap):
(add-after 'unpack 'unpack-submodule-sources
(lambda* (#:key inputs #:allow-other-keys)
(mkdir "../opencv-extra")
(mkdir "../opencv-contrib")
- (let ((unpack (lambda (source target)
- (with-directory-excursion target
- (apply invoke "unzip"
- (list (assoc-ref inputs source)))))))
- (unpack "opencv-extra" "../opencv-extra")
- (unpack "opencv-contrib" "../opencv-contrib"))))
+ (copy-recursively (assoc-ref inputs "opencv-extra")
+ "../opencv-extra")
+ (invoke "tar" "xvf"
+ (assoc-ref inputs "opencv-contrib")
+ "--strip-components=1"
+ "-C" "../opencv-contrib")))
(add-after 'set-paths 'add-ilmbase-include-path
(lambda* (#:key inputs #:allow-other-keys)
;; Therefore we must do it.
(zero? (system (format #f "~a/bin/Xvfb ~a &" xorg-server disp)))))))))
(native-inputs
- `(("unzip" ,unzip)
- ("pkg-config" ,pkg-config)
- ("xorg-server" ,xorg-server) ; For running the tests
+ `(("pkg-config" ,pkg-config)
+ ("xorg-server" ,xorg-server-for-tests) ; For running the tests
("opencv-extra"
,(origin
- (method url-fetch)
- (uri (string-append "https://codeload.github.com/"
- "opencv/opencv_extra/zip/" version))
- (file-name (string-append "opencv-extra-" version ".zip"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/opencv/opencv_extra")
+ (commit version)))
+ (file-name (git-file-name "opencv_extra" version))
(sha256
- (base32 "0yd1vidzbg6himxyh4yzivywijg8548kfmcn421khabnipm7l74y"))))
+ (base32 "08p5xnq8n1jw8svvz0fnirfg7q8dm3p4a5dl7527s5xj0f9qn7lp"))))
("opencv-contrib"
,(origin
- (method url-fetch)
- (uri (string-append "https://codeload.github.com/"
- "opencv/opencv_contrib/zip/" version))
- (file-name (string-append "opencv-contrib-" version ".zip"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/opencv/opencv_contrib")
+ (commit version)))
+ (file-name (git-file-name "opencv_contrib" version))
+ (patches (search-patches "opencv-rgbd-aarch64-test-fix.patch"))
(sha256
- (base32 "0j0ci6ia1qwklp9hq07ypl0vkngj1wrgh6n98n657m5d0pyp4m0g"))))))
+ (base32 "1f334glf39nk42mpqq6j732h3ql2mpz89jd4mcl678s8n73nfjh2"))))))
(inputs `(("libjpeg" ,libjpeg)
("libpng" ,libpng)
("jasper" ,jasper)
(define-public vips
(package
(name "vips")
- (version "8.7.1")
- (source (origin
- (method url-fetch)
- (uri (string-append
- "https://github.com/libvips/libvips/releases/download/v"
- version "/vips-" version ".tar.gz"))
- (sha256
- (base32 "1w3b90pdw7nj2p0gb4f96h6zhmga513f968ldfhz1rkhg7y81c0s"))))
+ (version "8.7.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/libvips/libvips/releases/download/v"
+ version "/vips-" version ".tar.gz"))
+ (sha256
+ (base32 "01gjhcrl6zj7mcj1al717v5jsniahplqhz1xkfh2j78vyfl1hxff"))))
(build-system gnu-build-system)
(native-inputs
`(("pkg-config" ,pkg-config)
("expat" ,expat)
("hdf5" ,hdf5)))
(home-page "https://libvips.github.io/libvips/")
- (synopsis "Image processing system")
+ (synopsis "Multithreaded image processing system with low memory needs")
(description
- "vips is a demand-driven, horizontally threaded image processing library.")
+ "VIPS is a demand-driven, horizontally threaded image processing library.
+It's particularly good at processing large images, working with colour,
+scientific analysis, and general research & development.
+
+Compared to most image processing libraries VIPS needs little RAM and runs
+quickly, especially on machines with more than one CPU core. This is primarily
+due to its architecture which automatically parallelises the image workflows.")
(license license:lgpl2.1+)))
(define-public nip2
(package
(name "nip2")
- (version "8.7.0")
+ (version "8.7.1")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/libvips/nip2/releases/download/v"
version "/nip2-" version ".tar.gz" ))
(sha256
- (base32 "08dxfds4n1vxdilxcw01741a2r6fxyhawi656b7f0hy6znnkbsbc"))))
+ (base32 "0l7n427njif53npqn02gfjjly8y3khbrkzqxp10j5vp9h97psgiw"))))
(build-system gnu-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
- ;; test_conv.ws keep failing so disabling for now
+ ;; test_conv.ws keep failing so disabling for now.
(add-after 'unpack 'disable-test-conv
(lambda _
(delete-file "test/workspaces/test_conv.ws")
("gtk+-2" ,gtk+-2)
("libxml2" ,libxml2)
("libexif" ,libexif)
- ("libjpeg" ,libjpeg) ;required by vips.pc
+ ("libjpeg" ,libjpeg) ; required by vips.pc
("librsvg" ,librsvg)
("fftw" ,fftw)
("libgsf" ,libgsf)
create a set of formula connecting your objects together, and on a change nip2
recalculates.")
(license license:gpl2+)))
+
+(define-public vxl
+ (package
+ (name "vxl")
+ (version "2.0.2")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/vxl/vxl.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0949hw57szq8943f1whwqaz591xjmb19kj803hcv74hdai2b0ycg"))
+ (modules '((guix build utils)))
+ ;; TODO: vxl includes an old version of dcmtk. It won't build with
+ ;; version 3.6.x.
+ (snippet
+ '(begin
+ (for-each delete-file-recursively
+ '("v3p/bzlib/"
+ "v3p/geotiff/"
+ "v3p/jpeg/"
+ "v3p/png/"
+ "v3p/tiff/"
+ "v3p/zlib/"))
+ (substitute* "v3p/CMakeLists.txt"
+ (("add_subdirectory\\((tiff|png|jpeg|zlib|bzlib|geotiff)\\)")
+ ""))
+ #t))))
+ (build-system cmake-build-system)
+ (inputs
+ `(("libgeotiff" ,libgeotiff)
+ ("libtiff" ,libtiff)
+ ("libjpeg" ,libjpeg)
+ ("libpng" ,libpng)
+ ("zlib" ,zlib)))
+ (home-page "https://github.com/vxl/vxl/")
+ (synopsis "Collection of C++ libraries for computer vision")
+ (description "VXL (the Vision-something-Libraries) is a collection of C++
+libraries designed for computer vision research and implementation.")
+ (license license:bsd-3)))
+
+(define-public vxl-1
+ (package (inherit vxl)
+ (name "vxl")
+ (version "1.18.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/vxl/vxl.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1g4mr2cc58jwm0vasscbd4y5380wj3ahkvq121z4gs83fhavvxgz"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ (for-each delete-file-recursively
+ '("v3p/bzlib/"
+ "v3p/geotiff/"
+ "v3p/png/"
+ "v3p/tiff/"
+ "v3p/zlib/"))
+ (substitute* "v3p/CMakeLists.txt"
+ (("add_subdirectory\\((tiff|png|jpeg|zlib|bzlib|geotiff)\\)")
+ ""))
+ #t))))
+ (arguments
+ `(#: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)
+ ("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)
+ ("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+)))
HCoop / jackhill / guix / guix.git / blobdiff