gnu/packages/image-processing.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2017 John Darrington <jmd@gnu.org>
   3 ;;; Copyright © 2017, 2019 Ricardo Wurmus <rekado@elephly.net>
   4 ;;; Copyright © 2014 Ludovic Courtès <ludo@gnu.org>
   5 ;;; Copyright © 2014 Mark H Weaver <mhw@netris.org>
   6 ;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.org>
   7 ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
   8 ;;; Copyright © 2018 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
   9 ;;; Copyright © 2018 Lprndn <guix@lprndn.info>
  10 ;;; Copyright © 2019 Efraim Flashner <efraim@flashner.co.il>
  11 ;;;
  12 ;;; This file is part of GNU Guix.
  13 ;;;
  14 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  15 ;;; under the terms of the GNU General Public License as published by
  16 ;;; the Free Software Foundation; either version 3 of the License, or (at
  17 ;;; your option) any later version.
  18 ;;;
  19 ;;; GNU Guix is distributed in the hope that it will be useful, but
  20 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  21 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  22 ;;; GNU General Public License for more details.
  23 ;;;
  24 ;;; You should have received a copy of the GNU General Public License
  25 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  26
  27 (define-module (gnu packages image-processing)
  28   #:use-module ((guix licenses) #:prefix license:)
  29   #:use-module (guix packages)
  30   #:use-module (guix utils)
  31   #:use-module (guix download)
  32   #:use-module (guix git-download)
  33   #:use-module (guix build-system cmake)
  34   #:use-module (guix build-system gnu)
  35   #:use-module (gnu packages)
  36   #:use-module (gnu packages algebra)
  37   #:use-module (gnu packages bison)
  38   #:use-module (gnu packages boost)
  39   #:use-module (gnu packages check)
  40   #:use-module (gnu packages compression)
  41   #:use-module (gnu packages curl)
  42   #:use-module (gnu packages documentation)
  43   #:use-module (gnu packages flex)
  44   #:use-module (gnu packages fontutils)
  45   #:use-module (gnu packages geo)
  46   #:use-module (gnu packages ghostscript)
  47   #:use-module (gnu packages gl)
  48   #:use-module (gnu packages glib)
  49   #:use-module (gnu packages gnome)
  50   #:use-module (gnu packages graphics)
  51   #:use-module (gnu packages graphviz)
  52   #:use-module (gnu packages gstreamer)
  53   #:use-module (gnu packages gtk)
  54   #:use-module (gnu packages image)
  55   #:use-module (gnu packages imagemagick)
  56   #:use-module (gnu packages maths)
  57   #:use-module (gnu packages pdf)
  58   #:use-module (gnu packages perl)
  59   #:use-module (gnu packages photo)
  60   #:use-module (gnu packages pkg-config)
  61   #:use-module (gnu packages protobuf)
  62   #:use-module (gnu packages python)
  63   #:use-module (gnu packages python-xyz)
  64   #:use-module (gnu packages qt)
  65   #:use-module (gnu packages serialization)
  66   #:use-module (gnu packages tbb)
  67   #:use-module (gnu packages tls)
  68   #:use-module (gnu packages video)
  69   #:use-module (gnu packages xiph)
  70   #:use-module (gnu packages xml)
  71   #:use-module (gnu packages xorg)
  72   #:use-module (ice-9 match)
  73   #:use-module (srfi srfi-1))
  74
  75 (define-public dcmtk
  76   (package
  77     (name "dcmtk")
  78     (version "3.6.4")
  79     (source
  80      (origin
  81        (method url-fetch)
  82        (uri
  83         (string-append "ftp://dicom.offis.de/pub/dicom/offis/software/dcmtk/"
  84                        "dcmtk" (string-join (string-split version #\.) "")
  85                        "/dcmtk-" version ".tar.gz"))
  86        (sha256
  87         (base32 "1h22z8g0kmvhg8lgkbikyzyphhvxvq6018a00yd6i4g0z9ag6gx9"))))
  88     (build-system cmake-build-system)
  89     (inputs
  90      `(;; Our ICU is too recent: “error: ‘UChar’ does not name a type“.
  91        ;; ("icu4c" ,icu4c)
  92        ("libjpeg" ,libjpeg)
  93        ("libpng" ,libpng)
  94        ("libtiff" ,libtiff)
  95        ("libxml2" ,libxml2)
  96        ("openssl" ,openssl)
  97        ("zlib" ,zlib)))
  98     (native-inputs
  99      `(("doxygen" ,doxygen)))           ; for HTML documentation
 100     (home-page "https://dcmtk.org")
 101     (synopsis "Libraries and programs implementing parts of the DICOM standard")
 102     (description "DCMTK is a collection of libraries and applications
 103 implementing large parts the DICOM standard.  It includes software for
 104 examining, constructing and converting DICOM image files, handling offline
 105 media, sending and receiving images over a network connection, as well as
 106 demonstrative image storage and worklist servers.")
 107     (license (license:fsf-free
 108               "file://COPYRIGHT"
 109               "A union of the Apache 2.0 licence and various non-copyleft
 110 licences similar to the Modified BSD licence."))))
 111
 112 (define-public mia
 113   (package
 114     (name "mia")
 115     (version "2.4.6")
 116     (source (origin
 117               (method url-fetch)
 118               (uri (string-append "mirror://sourceforge/mia/mia/"
 119                                   (version-major+minor version)
 120                                   "/mia-" version ".tar.xz"))
 121               (sha256
 122                (base32
 123                 "0j4nd5z7i3v199jh7hqqhwd4g7snchizkc7rhzanpvngqg91m1pb"))))
 124     (build-system cmake-build-system)
 125     (arguments
 126      `(#:configure-flags
 127        (list "-DMIA_CREATE_NIPYPE_INTERFACES=0"
 128              "-DCMAKE_CXX_FLAGS=-fpermissive")))
 129     (inputs
 130      `(("boost" ,boost)
 131        ("dcmtk" ,dcmtk)
 132        ("doxygen" ,doxygen)
 133        ("eigen" ,eigen)
 134        ("fftw" ,fftw)
 135        ("fftwf" ,fftwf)
 136        ("gsl" ,gsl)
 137        ("gts" ,gts)
 138        ("hdf5" ,hdf5)
 139        ("itpp" ,itpp)
 140        ("libjpeg" ,libjpeg)
 141        ("libpng" ,libpng)
 142        ("libtiff" ,libtiff)
 143        ("libxml" ,libxml2)
 144        ("libxml++" ,libxml++)
 145        ("maxflow" ,maxflow)
 146        ("niftilib" ,niftilib)
 147        ("nlopt" ,nlopt)
 148        ("openexr" ,openexr)
 149        ("python-lxml" ,python2-lxml)
 150        ("vtk" ,vtk)))
 151     (native-inputs
 152      `(("pkg-config" ,pkg-config)
 153        ("python" ,python-2)))
 154     (home-page "http://mia.sourceforge.net")
 155     (synopsis "Toolkit for gray scale medical image analysis")
 156     (description "MIA provides a combination of command line tools, plug-ins,
 157 and libraries that make it possible run image processing tasks interactively
 158 in a command shell and to prototype using the shell's scripting language.  It
 159 is built around a plug-in structure that makes it easy to add functionality
 160 without compromising the original code base and it makes use of a wide variety
 161 of external libraries that provide additional functionality.")
 162     (license license:gpl3+)))
 163
 164 (define-public vtk
 165   (package
 166     (name "vtk")
 167     (version "8.2.0")
 168     (source (origin
 169               (method url-fetch)
 170               (uri (string-append "https://vtk.org/files/release/"
 171                                   (version-major+minor version)
 172                                   "/VTK-" version ".tar.gz"))
 173               (sha256
 174                (base32
 175                 "1fspgp8k0myr6p2a6wkc21ldcswb4bvmb484m12mxgk1a9vxrhrl"))))
 176     (build-system cmake-build-system)
 177     (arguments
 178      '(#:build-type "Release"           ;Build without '-g' to save space.
 179        ;; -DVTK_USE_SYSTEM_NETCDF:BOOL=TRUE requires netcdf_cxx
 180        #:configure-flags '("-DVTK_USE_SYSTEM_EXPAT:BOOL=TRUE"
 181                            "-DVTK_USE_SYSTEM_FREETYPE:BOOL=TRUE"
 182                            "-DVTK_USE_SYSTEM_HDF5:BOOL=TRUE"
 183                            "-DVTK_USE_SYSTEM_JPEG:BOOL=TRUE"
 184                            "-DVTK_USE_SYSTEM_JSONCPP:BOOL=TRUE"
 185                            "-DVTK_USE_SYSTEM_LIBXML2:BOOL=TRUE"
 186                            "-DVTK_USE_SYSTEM_OGGTHEORA:BOOL=TRUE"
 187                            "-DVTK_USE_SYSTEM_PNG:BOOL=TRUE"
 188                            "-DVTK_USE_SYSTEM_TIFF:BOOL=TRUE"
 189                            "-DVTK_USE_SYSTEM_ZLIB:BOOL=TRUE")
 190        #:tests? #f))                              ;XXX: no "test" target
 191     (inputs
 192      `(("libXt" ,libxt)
 193        ("xorgproto" ,xorgproto)
 194        ("libX11" ,libx11)
 195        ("libxml2" ,libxml2)
 196        ("mesa" ,mesa)
 197        ("glu" ,glu)
 198        ("expat" ,expat)
 199        ("freetype" ,freetype)
 200        ("hdf5" ,hdf5)
 201        ("jpeg" ,libjpeg)
 202        ("jsoncpp" ,jsoncpp)
 203        ("libogg" ,libogg)
 204        ("libtheora" ,libtheora)
 205        ("png" ,libpng)
 206        ("tiff" ,libtiff)
 207        ("zlib" ,zlib)))
 208     (home-page "https://vtk.org/")
 209     (synopsis "Libraries for 3D computer graphics")
 210     (description
 211      "The Visualization Toolkit (VTK) is a C++ library for 3D computer graphics,
 212 image processing and visualization.  It supports a wide variety of
 213 visualization algorithms including: scalar, vector, tensor, texture, and
 214 volumetric methods; and advanced modeling techniques such as: implicit
 215 modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay
 216 triangulation.  VTK has an extensive information visualization framework, has
 217 a suite of 3D interaction widgets, supports parallel processing, and
 218 integrates with various databases on GUI toolkits such as Qt and Tk.")
 219     (license license:bsd-3)))
 220
 221 ;; itksnap needs an older variant of VTK.
 222 (define-public vtk-6
 223   (package (inherit vtk)
 224     (version "6.3.0")
 225     (source (origin
 226               (method url-fetch)
 227               (uri (string-append "https://vtk.org/files/release/"
 228                                   (version-major+minor version)
 229                                   "/VTK-" version ".tar.gz"))
 230               (sha256
 231                (base32
 232                 "0pla1r5mvkgl4sl213gfdhzrypdgai0h3z5mfgm6p9jz9hsr794j"))))
 233     (inputs
 234      `(("jsoncpp" ,jsoncpp-for-tensorflow)
 235        ,@(alist-delete "jsoncpp" (package-inputs vtk))))))
 236
 237 (define-public opencv
 238   (package
 239     (name "opencv")
 240     (version "3.4.3")
 241     (source (origin
 242               (method git-fetch)
 243               (uri (git-reference
 244                      (url "https://github.com/opencv/opencv")
 245                      (commit version)))
 246               (file-name (git-file-name name version))
 247               (sha256
 248                (base32
 249                 "06bc61r8myym4s8im10brdjfg4wxkrvsbhhl7vr1msdan2xddzi3"))
 250               (modules '((guix build utils)))
 251               (snippet
 252                '(begin
 253                   ;; Remove external libraries. We have all available in Guix:
 254                   (delete-file-recursively "3rdparty")
 255
 256                   ;; Milky icon set is non-free:
 257                   (delete-file-recursively "modules/highgui/src/files_Qt/Milky")
 258
 259                   ;; Some jars found:
 260                   (for-each delete-file
 261                             '("modules/java/test/pure_test/lib/junit-4.11.jar"
 262                               "samples/java/sbt/sbt/sbt-launch.jar"))
 263                   #t))))
 264     (build-system cmake-build-system)
 265     (arguments
 266      `(#:configure-flags
 267        (list "-DWITH_IPP=OFF"
 268              "-DWITH_ITT=OFF"
 269              "-DWITH_CAROTENE=OFF" ; only visible on arm/aarch64
 270              "-DENABLE_PRECOMPILED_HEADERS=OFF"
 271
 272              ;; FIXME: OpenEXR requires C++11 or later.  Remove this when
 273              ;; the default compiler is GCC 7.
 274              "-DCMAKE_CXX_FLAGS=-std=gnu++11"
 275
 276              ;; CPU-Features:
 277              ;; See cmake/OpenCVCompilerOptimizations.cmake
 278              ;; (CPU_ALL_OPTIMIZATIONS) for a list of all optimizations
 279              ;; BASELINE is the minimum optimization all CPUs must support
 280              ;;
 281              ;; DISPATCH is the list of optional dispatches.
 282              "-DCPU_BASELINE=SSE2"
 283
 284              ,@(match (%current-system)
 285                  ("x86_64-linux"
 286                   '("-DCPU_DISPATCH=NEON;VFPV3;FP16;SSE;SSE2;SSE3;SSSE3;SSE4_1;SSE4_2;POPCNT;AVX;FP16;AVX2;FMA3;AVX_512F;AVX512_SKX"
 287                     "-DCPU_DISPATCH_REQUIRE=SSE3,SSSE3,SSE4_1,SSE4_2,AVX,AVX2"))
 288                  ("armhf-linux"
 289                   '("-DCPU_BASELINE_DISABLE=NEON")) ; causes build failures
 290                  ("aarch64-linux"
 291                   '("-DCPU_BASELINE=NEON"
 292                     "-DCPU_DISPATCH=NEON;VFPV3;FP16"))
 293                  (_ '()))
 294
 295              "-DBUILD_PERF_TESTS=OFF"
 296              "-DBUILD_TESTS=ON"
 297
 298              (string-append "-DOPENCV_EXTRA_MODULES_PATH=" (getcwd)
 299                             "/opencv-contrib/modules")
 300
 301              ;;Define test data:
 302              (string-append "-DOPENCV_TEST_DATA_PATH=" (getcwd)
 303                             "/opencv-extra/testdata")
 304
 305              ;; Is ON by default and would try to rebuild 3rd-party protobuf,
 306              ;; which we had removed, which would lead to an error:
 307              "-DBUILD_PROTOBUF=OFF"
 308
 309              ;; Rebuild protobuf files, because we have a slightly different
 310              ;; version than the included one. If we would not update, we
 311              ;; would get a compile error later:
 312              "-DPROTOBUF_UPDATE_FILES=ON"
 313
 314              ;; xfeatures2d disabled, because it downloads extra binaries from
 315              ;; https://github.com/opencv/opencv_3rdparty
 316              ;; defined in xfeatures2d/cmake/download_{vgg|bootdesc}.cmake
 317              ;; Cmp this bug entry:
 318              ;; https://github.com/opencv/opencv_contrib/issues/1131
 319              "-DBUILD_opencv_xfeatures2d=OFF")
 320        #:phases
 321        (modify-phases %standard-phases
 322          (add-after 'unpack 'disable-broken-tests
 323            (lambda _
 324              ;; These tests fails with:
 325              ;; vtkXOpenGLRenderWindow (0x723990): Could not find a decent config
 326              ;; I think we have no OpenGL support with the Xvfb.
 327              (substitute* '("modules/viz/test/test_tutorial3.cpp"
 328                             "modules/viz/test/test_main.cpp"
 329                             "modules/viz/test/tests_simple.cpp"
 330                             "modules/viz/test/test_viz3d.cpp")
 331                (("(TEST\\(Viz, )([a-z].*\\).*)" all pre post)
 332                 (string-append pre "DISABLED_" post)))
 333
 334              ;; This one fails with "unknown file: Failure"
 335              ;; But I couldn't figure out which file was missing:
 336              (substitute* "../opencv-contrib/modules/face/test/test_face_align.cpp"
 337                (("(TEST\\(CV_Face_FacemarkKazemi, )(can_detect_landmarks\\).*)"
 338                  all pre post)
 339                 (string-append pre "DISABLED_" post)))
 340
 341              ;; Failure reason: Bad accuracy
 342              ;; Incorrect count of accurate poses [2nd case]: 90.000000 / 94.000000
 343              (substitute* "../opencv-contrib/modules/rgbd/test/test_odometry.cpp"
 344                (("(TEST\\(RGBD_Odometry_Rgbd, )(algorithmic\\).*)" all pre post)
 345                 (string-append pre "DISABLED_" post)))
 346              #t))
 347
 348          (add-after 'unpack 'unpack-submodule-sources
 349            (lambda* (#:key inputs #:allow-other-keys)
 350              (mkdir "../opencv-extra")
 351              (mkdir "../opencv-contrib")
 352              (copy-recursively (assoc-ref inputs "opencv-extra")
 353                                "../opencv-extra")
 354              (invoke "tar" "xvf"
 355                      (assoc-ref inputs "opencv-contrib")
 356                      "--strip-components=1"
 357                      "-C" "../opencv-contrib")))
 358
 359          (add-after 'set-paths 'add-ilmbase-include-path
 360            (lambda* (#:key inputs #:allow-other-keys)
 361            ;; OpenEXR propagates ilmbase, but its include files do not appear
 362            ;; in the CPATH, so we need to add "$ilmbase/include/OpenEXR/" to
 363            ;; the CPATH to satisfy the dependency on "ImathVec.h".
 364            (setenv "CPATH"
 365                    (string-append (assoc-ref inputs "ilmbase")
 366                                   "/include/OpenEXR"
 367                                   ":" (or (getenv "CPATH") "")))
 368            #t))
 369        (add-before 'check 'start-xserver
 370          (lambda* (#:key inputs #:allow-other-keys)
 371            (let ((xorg-server (assoc-ref inputs "xorg-server"))
 372                  (disp ":1"))
 373              (setenv "HOME" (getcwd))
 374              (setenv "DISPLAY" disp)
 375              ;; There must be a running X server and make check doesn't start one.
 376              ;; Therefore we must do it.
 377              (zero? (system (format #f "~a/bin/Xvfb ~a &" xorg-server disp)))))))))
 378     (native-inputs
 379      `(("pkg-config" ,pkg-config)
 380        ("xorg-server" ,xorg-server) ; For running the tests
 381        ("opencv-extra"
 382         ,(origin
 383            (method git-fetch)
 384            (uri (git-reference
 385                   (url "https://github.com/opencv/opencv_extra")
 386                   (commit version)))
 387            (file-name (git-file-name "opencv_extra" version))
 388            (sha256
 389             (base32 "08p5xnq8n1jw8svvz0fnirfg7q8dm3p4a5dl7527s5xj0f9qn7lp"))))
 390        ("opencv-contrib"
 391         ,(origin
 392            (method git-fetch)
 393            (uri (git-reference
 394                   (url "https://github.com/opencv/opencv_contrib")
 395                   (commit version)))
 396            (file-name (git-file-name "opencv_contrib" version))
 397            (patches (search-patches "opencv-rgbd-aarch64-test-fix.patch"))
 398            (sha256
 399             (base32 "1f334glf39nk42mpqq6j732h3ql2mpz89jd4mcl678s8n73nfjh2"))))))
 400     (inputs `(("libjpeg" ,libjpeg)
 401               ("libpng" ,libpng)
 402               ("jasper" ,jasper)
 403               ;; ffmpeg 4.0 causes core dumps in tests.
 404               ("ffmpeg" ,ffmpeg-3.4)
 405               ("libtiff" ,libtiff)
 406               ("hdf5" ,hdf5)
 407               ("libgphoto2" ,libgphoto2)
 408               ("libwebp" ,libwebp)
 409               ("zlib" ,zlib)
 410               ("gtkglext" ,gtkglext)
 411               ("openexr" ,openexr)
 412               ("ilmbase" ,ilmbase)
 413               ("gtk+" ,gtk+-2)
 414               ("python-numpy" ,python-numpy)
 415               ("protobuf" ,protobuf)
 416               ("vtk" ,vtk)
 417               ("python" ,python)))
 418     ;; These three CVEs are not a problem of OpenCV, see:
 419     ;; https://github.com/opencv/opencv/issues/10998
 420     (properties '((lint-hidden-cve . ("CVE-2018-7712"
 421                                       "CVE-2018-7713"
 422                                       "CVE-2018-7714"))))
 423     (synopsis "Computer vision library")
 424     (description "OpenCV is a library aimed at
 425 real-time computer vision, including several hundred computer
 426 vision algorithms.  It can be used to do things like:
 427
 428 @itemize
 429 @item image and video input and output
 430 @item image and video processing
 431 @item displaying
 432 @item feature recognition
 433 @item segmentation
 434 @item facial recognition
 435 @item stereo vision
 436 @item structure from motion
 437 @item augmented reality
 438 @item machine learning
 439 @end itemize\n")
 440     (home-page "https://opencv.org/")
 441     (license license:bsd-3)))
 442
 443 (define-public vips
 444   (package
 445     (name "vips")
 446     (version "8.7.4")
 447     (source
 448      (origin
 449        (method url-fetch)
 450        (uri (string-append
 451              "https://github.com/libvips/libvips/releases/download/v"
 452              version "/vips-" version ".tar.gz"))
 453        (sha256
 454         (base32 "01gjhcrl6zj7mcj1al717v5jsniahplqhz1xkfh2j78vyfl1hxff"))))
 455     (build-system gnu-build-system)
 456     (native-inputs
 457      `(("pkg-config" ,pkg-config)
 458        ("gobject-introspection" ,gobject-introspection)))
 459     (inputs
 460      `(("glib" ,glib)
 461        ("libjpeg" ,libjpeg)
 462        ("libpng" ,libpng)
 463        ("librsvg" ,librsvg)
 464        ("libtiff" ,libtiff)
 465        ("libexif" ,libexif)
 466        ("giflib" ,giflib)
 467        ("libgsf" ,libgsf)
 468        ("fftw" ,fftw)
 469        ("poppler" ,poppler)
 470        ("pango" ,pango)
 471        ("lcms" ,lcms)
 472        ("matio" ,matio)
 473        ("libwebp" ,libwebp)
 474        ("niftilib" ,niftilib)
 475        ("openexr" ,openexr)
 476        ("orc" ,orc)
 477        ("imagemagick" ,imagemagick)
 478        ("libxml2" ,libxml2)
 479        ("expat" ,expat)
 480        ("hdf5" ,hdf5)))
 481     (home-page "https://libvips.github.io/libvips/")
 482     (synopsis "Multithreaded image processing system with low memory needs")
 483     (description
 484      "VIPS is a demand-driven, horizontally threaded image processing library.
 485 It's particularly good at processing large images, working with colour,
 486 scientific analysis, and general research & development.
 487
 488 Compared to most image processing libraries VIPS needs little RAM and runs
 489 quickly, especially on machines with more than one CPU core.  This is primarily
 490 due to its architecture which automatically parallelises the image workflows.")
 491     (license license:lgpl2.1+)))
 492
 493 (define-public nip2
 494   (package
 495     (name "nip2")
 496     (version "8.7.1")
 497     (source
 498      (origin
 499        (method url-fetch)
 500        (uri (string-append "https://github.com/libvips/nip2/releases/download/v"
 501                            version "/nip2-" version ".tar.gz" ))
 502        (sha256
 503         (base32 "0l7n427njif53npqn02gfjjly8y3khbrkzqxp10j5vp9h97psgiw"))))
 504     (build-system gnu-build-system)
 505     (arguments
 506      `(#:phases
 507        (modify-phases %standard-phases
 508          ;; test_conv.ws keep failing so disabling for now.
 509          (add-after 'unpack 'disable-test-conv
 510            (lambda _
 511              (delete-file "test/workspaces/test_conv.ws")
 512              #t))
 513          (add-before 'check 'set-home
 514            (lambda _
 515              (setenv "HOME" "/tmp") #t)))))
 516     (inputs
 517      `(("vips" ,vips)
 518        ("glib" ,glib)
 519        ("libtiff" ,libtiff)
 520        ("gtk+-2" ,gtk+-2)
 521        ("libxml2" ,libxml2)
 522        ("libexif" ,libexif)
 523        ("libjpeg" ,libjpeg)             ; required by vips.pc
 524        ("librsvg" ,librsvg)
 525        ("fftw" ,fftw)
 526        ("libgsf" ,libgsf)
 527        ("imagemagick" ,imagemagick)
 528        ("orc" ,orc)
 529        ("matio" ,matio)
 530        ("lcms" ,lcms)
 531        ("libwebp" ,libwebp)
 532        ("openexr" ,openexr)
 533        ("poppler" ,poppler)
 534        ("gsl" ,gsl)))
 535     (native-inputs
 536      `(("flex" ,flex)
 537        ("bison" ,bison)
 538        ("pkg-config" ,pkg-config)))
 539     (home-page "https://github.com/libvips/nip2")
 540     (synopsis "Spreadsheet-like GUI for libvips")
 541     (description "This package provide a graphical user interface (GUI) for
 542 the VIPS image processing library.  It's a little like a spreadsheet: you
 543 create a set of formula connecting your objects together, and on a change nip2
 544 recalculates.")
 545     (license license:gpl2+)))
 546
 547 (define-public vxl
 548   (package
 549     (name "vxl")
 550     (version "2.0.2")
 551     (source
 552      (origin
 553        (method git-fetch)
 554        (uri (git-reference
 555              (url "https://github.com/vxl/vxl.git")
 556              (commit (string-append "v" version))))
 557        (file-name (git-file-name name version))
 558        (sha256
 559         (base32 "0949hw57szq8943f1whwqaz591xjmb19kj803hcv74hdai2b0ycg"))
 560        (modules '((guix build utils)))
 561        ;; TODO: vxl includes an old version of dcmtk.  It won't build with
 562        ;; version 3.6.x.
 563        (snippet
 564         '(begin
 565            (for-each delete-file-recursively
 566                      '("v3p/bzlib/"
 567                        "v3p/geotiff/"
 568                        "v3p/jpeg/"
 569                        "v3p/png/"
 570                        "v3p/tiff/"
 571                        "v3p/zlib/"))
 572            (substitute* "v3p/CMakeLists.txt"
 573              (("add_subdirectory\\((tiff|png|jpeg|zlib|bzlib|geotiff)\\)")
 574               ""))
 575            #t))))
 576     (build-system cmake-build-system)
 577     (inputs
 578      `(("libgeotiff" ,libgeotiff)
 579        ("libtiff" ,libtiff)
 580        ("libjpeg" ,libjpeg)
 581        ("libpng" ,libpng)
 582        ("zlib" ,zlib)))
 583     (home-page "https://github.com/vxl/vxl/")
 584     (synopsis "Collection of C++ libraries for computer vision")
 585     (description "VXL (the Vision-something-Libraries) is a collection of C++
 586 libraries designed for computer vision research and implementation.")
 587     (license license:bsd-3)))
 588
 589 (define-public vxl-1
 590   (package (inherit vxl)
 591     (name "vxl")
 592     (version "1.18.0")
 593     (source
 594      (origin
 595        (method git-fetch)
 596        (uri (git-reference
 597              (url "https://github.com/vxl/vxl.git")
 598              (commit (string-append "v" version))))
 599        (file-name (git-file-name name version))
 600        (sha256
 601         (base32 "1g4mr2cc58jwm0vasscbd4y5380wj3ahkvq121z4gs83fhavvxgz"))
 602        (modules '((guix build utils)))
 603        (snippet
 604         '(begin
 605            (for-each delete-file-recursively
 606                      '("v3p/bzlib/"
 607                        "v3p/geotiff/"
 608                        "v3p/png/"
 609                        "v3p/tiff/"
 610                        "v3p/zlib/"))
 611            (substitute* "v3p/CMakeLists.txt"
 612              (("add_subdirectory\\((tiff|png|jpeg|zlib|bzlib|geotiff)\\)")
 613               ""))
 614            #t))))
 615     (arguments
 616      `(#:configure-flags
 617        ;; Needed for itk-snap
 618        (list "-DVNL_CONFIG_LEGACY_METHODS=ON")))))
 619
 620 (define-public insight-toolkit
 621   (package
 622     (name "insight-toolkit")
 623     (version "5.0.0")
 624     (source
 625      (origin
 626        (method url-fetch)
 627        (uri (string-append "https://github.com/InsightSoftwareConsortium/ITK/"
 628                            "releases/download/v" version "/InsightToolkit-"
 629                            version ".tar.xz"))
 630        (sha256
 631         (base32 "0bs63mk4q8jmx38f031jy5w5n9yy5ng9x8ijwinvjyvas8cichqi"))))
 632     (build-system cmake-build-system)
 633     (arguments
 634      `(#:tests? #f            ; tests require network access and external data
 635        #:configure-flags
 636        '("-DITK_USE_GPU=ON"
 637          "-DITK_USE_SYSTEM_LIBRARIES=ON"
 638          "-DITK_USE_SYSTEM_GOOGLETEST=ON"
 639          "-DITK_BUILD_SHARED=ON"
 640          ;; This prevents "GTest::GTest" from being added to the ITK_LIBRARIES
 641          ;; variable in the installed CMake files.  This is necessary as other
 642          ;; packages using insight-toolkit could not be configured otherwise.
 643          "-DGTEST_ROOT=gtest")
 644        #:phases
 645        (modify-phases %standard-phases
 646          (add-after 'unpack 'do-not-tune
 647            (lambda _
 648              (substitute* "CMake/ITKSetStandardCompilerFlags.cmake"
 649                (("-mute=native") ""))
 650              #t)))))
 651     (inputs
 652      `(("eigen" ,eigen)
 653        ("expat" ,expat)
 654        ("fftw" ,fftw)
 655        ("fftwf" ,fftwf)
 656        ("hdf5" ,hdf5)
 657        ("libjpeg" ,libjpeg)
 658        ("libpng" ,libpng)
 659        ("libtiff" ,libtiff)
 660        ("mesa" ,mesa-opencl)
 661        ("perl" ,perl)
 662        ("python" ,python)
 663        ("tbb" ,tbb)
 664        ("vxl" ,vxl-1)
 665        ("zlib" ,zlib)))
 666     (native-inputs
 667      `(("googletest" ,googletest)
 668        ("pkg-config" ,pkg-config)))
 669     (home-page "https://github.com/InsightSoftwareConsortium/ITK/")
 670     (synopsis "Scientific image processing, segmentation and registration")
 671     (description "The Insight Toolkit (ITK) is a toolkit for N-dimensional
 672 scientific image processing, segmentation, and registration.  Segmentation is
 673 the process of identifying and classifying data found in a digitally sampled
 674 representation.  Typically the sampled representation is an image acquired
 675 from such medical instrumentation as CT or MRI scanners.  Registration is the
 676 task of aligning or developing correspondences between data.  For example, in
 677 the medical environment, a CT scan may be aligned with a MRI scan in order to
 678 combine the information contained in both.")
 679     (license license:asl2.0)))
 680
 681 (define-public insight-toolkit-4
 682   (package (inherit insight-toolkit)
 683     (version "4.13.2")
 684     (source
 685      (origin
 686        (method url-fetch)
 687        (uri (string-append "https://github.com/InsightSoftwareConsortium/ITK/"
 688                            "releases/download/v" version "/InsightToolkit-"
 689                            version ".tar.xz"))
 690        (sha256
 691         (base32 "19cgfpd63gqrvc3m27m394gy2d7w79g5y6lvznb5qqr49lihbgns"))))
 692     (arguments
 693      `(#:tests? #f            ; tests require network access and external data
 694        #:configure-flags
 695        '("-DITKV3_COMPATIBILITY=ON"     ; needed for itk-snap
 696          "-DITK_USE_GPU=ON"
 697          "-DITK_USE_SYSTEM_LIBRARIES=ON"
 698          "-DITK_USE_SYSTEM_GOOGLETEST=ON"
 699          "-DITK_USE_SYSTEM_VXL=ON")))))
 700
 701 (define-public insight-toolkit-4.12
 702   (package (inherit insight-toolkit-4)
 703     (version "4.12.2")
 704     (source
 705      (origin
 706        (method url-fetch)
 707        (uri (string-append "mirror://sourceforge/itk/itk/4.12/"
 708                            "InsightToolkit-" version ".tar.xz"))
 709        (sha256
 710         (base32 "1qw9mxbh083siljygahl4gdfv91xvfd8hfl7ghwii19f60xrvn2w"))))))
 711
 712 (define-public itk-snap
 713   (package
 714     (name "itk-snap")
 715     (version "3.8.0")
 716     (source
 717      (origin
 718        (method git-fetch)
 719        (uri (git-reference
 720              (url "https://git.code.sf.net/p/itk-snap/src")
 721              (commit (string-append "v" version))))
 722        (file-name (git-file-name name version))
 723        (sha256
 724         (base32 "15i5ixpryfrbf3vrrb5rici8fb585f25k0v1ljds16bp1f1msr4q"))))
 725     (build-system cmake-build-system)
 726     (arguments
 727      `(#:configure-flags
 728        (list "-DSNAP_VERSION_GIT_SHA1=release"
 729              "-DSNAP_VERSION_GIT_BRANCH=release"
 730              "-DSNAP_VERSION_GIT_TIMESTAMP=0"
 731              "-DSNAP_PACKAGE_QT_PLUGINS=OFF"
 732              "-DCMAKE_POSITION_INDEPENDENT_CODE=ON"
 733              "-DCMAKE_CXX_FLAGS=-std=gnu++11 -fpermissive")
 734        #:phases
 735        (modify-phases %standard-phases
 736          ;; During the installation phase all libraries provided by all
 737          ;; dependencies will be copied to the lib directory.  That's insane,
 738          ;; so we disable this.
 739          (add-after 'unpack 'do-not-copy-dependencies
 740            (lambda _
 741              (substitute* "CMakeLists.txt"
 742                (("install_qt5_executable\
 743 \\(\\$\\{SNAP_MAIN_INSTALL_DIR\\}/\\$\\{SNAP_EXE\\}\\)")
 744                 ""))
 745              #t))
 746          (add-after 'unpack 'disable-gui-tests
 747            (lambda _
 748              ;; The GUI tests just time out.
 749              (substitute* "CMakeLists.txt"
 750                (("  (Workspace|DiffSpace|ProbeIntensity|RegionCompetition\
 751 |RandomForest|RandomForestBailOut)")
 752                 ""))
 753              #t))
 754          (add-after 'unpack 'make-reproducible
 755            (lambda _
 756              (substitute* "CMakeLists.txt"
 757                (("TODAY\\(SNAP_VERSION_COMPILE_DATE\\)")
 758                 "SET(SNAP_VERSION_COMPILE_DATE \"(removed for reproducibility)\")"))
 759              #t))
 760          (add-after 'unpack 'prepare-submodules
 761            (lambda* (#:key inputs #:allow-other-keys)
 762              (rmdir "Submodules/c3d")
 763              (copy-recursively (assoc-ref inputs "c3d-src")
 764                                "Submodules/c3d")
 765              (substitute* '("Submodules/c3d/adapters/BiasFieldCorrectionN4.cxx"
 766                             "Submodules/c3d/adapters/ApplyMetric.cxx")
 767                (("vcl_") "std::"))
 768              (rmdir "Submodules/greedy")
 769              (symlink (assoc-ref inputs "greedy-src")
 770                       "Submodules/greedy")
 771              #t))
 772          (add-after 'unpack 'fix-includes
 773            (lambda _
 774              (substitute* "GUI/Model/RegistrationModel.cxx"
 775                (("<vnl_symmetric_eigensystem.h>")
 776                 "<vnl/algo/vnl_symmetric_eigensystem.h>"))
 777              #t))
 778          (add-before 'check 'prepare-tests
 779            (lambda _
 780              ;; Needed by at least one test.
 781              (setenv "HOME" "/tmp")
 782              #t))
 783          (add-after 'install 'wrap-executable
 784            (lambda* (#:key inputs outputs #:allow-other-keys)
 785              (let ((out (assoc-ref outputs "out")))
 786                (wrap-program (string-append out "/bin/itksnap")
 787                  `("QT_PLUGIN_PATH" ":" prefix
 788                    ,(map (lambda (label)
 789                            (string-append (assoc-ref inputs label)
 790                                           "/lib/qt5/plugins"))
 791                          '("qtbase" "qtdeclarative"))))
 792                #t))))))
 793     (inputs
 794      `(("curl" ,curl)
 795        ("fftw" ,fftw)
 796        ("fftwf" ,fftwf)
 797        ("glu" ,glu)
 798        ("hdf5" ,hdf5)
 799        ("mesa" ,mesa-opencl)
 800        ;; This package does not build with either insight-toolkit 5.0.0 and
 801        ;; not with 4.13.  It really needs to be 4.12.
 802        ("itk" ,insight-toolkit-4.12)
 803        ("vtk" ,vtk-6)
 804        ("qtbase" ,qtbase)
 805        ("qtdeclarative" ,qtdeclarative)
 806        ("qttools" ,qttools)
 807        ("vxl" ,vxl-1)
 808        ("zlib" ,zlib)))
 809     (native-inputs
 810      `(("googletest" ,googletest)
 811        ("pkg-config" ,pkg-config)
 812        ("c3d-src"
 813         ,(let* ((commit "f521358db26e00002c911cc47bf463b043942ad3")
 814                 (revision "1")
 815                 (version (git-version "0" revision commit)))
 816            (origin
 817              (method git-fetch)
 818              (uri (git-reference
 819                    (url "https://github.com/pyushkevich/c3d.git")
 820                    (commit commit)))
 821              (file-name (git-file-name "c3d" version))
 822              (sha256
 823               (base32
 824                "0kyv3rxrxwr8c3sa9zv01lsnhk95b27gx1s870k3yi8qp52h7bx3")))))
 825        ;; We are using an arbitrary commit from 2017 because the latest
 826        ;; version breaks the build...
 827        ("greedy-src"
 828         ,(let* ((commit "97e340f7e8e66597599144947775e6039e79a0d3")
 829                 (revision "1")
 830                 (version (git-version "0" revision commit)))
 831            (origin
 832              (method git-fetch)
 833              (uri (git-reference
 834                    (url "https://github.com/pyushkevich/greedy.git")
 835                    (commit commit)))
 836              (file-name (git-file-name "greedy" version))
 837              (sha256
 838               (base32
 839                "0k5bc9za4jrc8z9dj08z1rkcp5xf0gnd1d2jmi1w9ny4vxh2q2ab")))))))
 840     (home-page "https://sourceforge.net/p/itk-snap/")
 841     (synopsis "Medical image segmentation")
 842     (description "ITK-SNAP is a tool for segmenting anatomical structures in
 843 medical images.  It provides an automatic active contour segmentation
 844 pipeline, along with supporting a manual segmentation toolbox.  ITK-SNAP has a
 845 full-featured UI aimed at clinical researchers.")
 846     ;; This includes the submodules greedy and c3d.
 847     (license license:gpl3+)))