Merge branch 'master' into core-updates

1 files changed, 326 insertions, 2 deletions

diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-processing.scm
index e708e1366c..b3972a2b76 100644
--- a/gnu/packages/image-processing.scm
+++ b/gnu/packages/image-processing.scm
@@ -1,6 +1,6 @@
 ;;; 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>
@@ -36,10 +36,13 @@
   #: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)
@@ -58,13 +61,16 @@
   #: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 (ice-9 match))
+  #:use-module (ice-9 match)
+  #:use-module (srfi srfi-1))
 
 (define-public dcmtk
   (package
@@ -212,6 +218,22 @@ a suite of 3D interaction widgets, supports parallel processing, and
 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")
@@ -517,3 +539,305 @@ the VIPS image processing library.  It's a little like a spreadsheet: you
 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"
+             "-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+)))