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, 2020 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 ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
  12 ;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
  13 ;;; Copyright © 2020 Pierre Neidhardt <mail@ambrevar.xyz>
  14 ;;;
  15 ;;; This file is part of GNU Guix.
  16 ;;;
  17 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  18 ;;; under the terms of the GNU General Public License as published by
  19 ;;; the Free Software Foundation; either version 3 of the License, or (at
  20 ;;; your option) any later version.
  21 ;;;
  22 ;;; GNU Guix is distributed in the hope that it will be useful, but
  23 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  24 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  25 ;;; GNU General Public License for more details.
  26 ;;;
  27 ;;; You should have received a copy of the GNU General Public License
  28 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  29
  30 (define-module (gnu packages image-processing)
  31   #:use-module ((guix licenses) #:prefix license:)
  32   #:use-module (guix packages)
  33   #:use-module (guix utils)
  34   #:use-module (guix download)
  35   #:use-module (guix git-download)
  36   #:use-module (guix build-system cmake)
  37   #:use-module (guix build-system gnu)
  38   #:use-module (gnu packages)
  39   #:use-module (gnu packages algebra)
  40   #:use-module (gnu packages bison)
  41   #:use-module (gnu packages boost)
  42   #:use-module (gnu packages check)
  43   #:use-module (gnu packages compression)
  44   #:use-module (gnu packages curl)
  45   #:use-module (gnu packages docbook)
  46   #:use-module (gnu packages documentation)
  47   #:use-module (gnu packages flex)
  48   #:use-module (gnu packages fontutils)
  49   #:use-module (gnu packages geo)
  50   #:use-module (gnu packages ghostscript)
  51   #:use-module (gnu packages gl)
  52   #:use-module (gnu packages glib)
  53   #:use-module (gnu packages gnome)
  54   #:use-module (gnu packages graphics)
  55   #:use-module (gnu packages graphviz)
  56   #:use-module (gnu packages gstreamer)
  57   #:use-module (gnu packages gtk)
  58   #:use-module (gnu packages image)
  59   #:use-module (gnu packages imagemagick)
  60   #:use-module (gnu packages maths)
  61   #:use-module (gnu packages pdf)
  62   #:use-module (gnu packages perl)
  63   #:use-module (gnu packages photo)
  64   #:use-module (gnu packages pkg-config)
  65   #:use-module (gnu packages protobuf)
  66   #:use-module (gnu packages python)
  67   #:use-module (gnu packages python-xyz)
  68   #:use-module (gnu packages qt)
  69   #:use-module (gnu packages serialization)
  70   #:use-module (gnu packages tbb)
  71   #:use-module (gnu packages tls)
  72   #:use-module (gnu packages version-control)
  73   #:use-module (gnu packages video)
  74   #:use-module (gnu packages xiph)
  75   #:use-module (gnu packages xml)
  76   #:use-module (gnu packages xorg)
  77   #:use-module (ice-9 match)
  78   #:use-module (srfi srfi-1))
  79
  80 (define-public dcmtk
  81   (package
  82     (name "dcmtk")
  83     (version "3.6.5")
  84     (source
  85      (origin
  86        (method url-fetch)
  87        (uri
  88         (string-append "ftp://dicom.offis.de/pub/dicom/offis/software/dcmtk/"
  89                        "dcmtk" (string-join (string-split version #\.) "")
  90                        "/dcmtk-" version ".tar.gz"))
  91        (sha256
  92         (base32 "1fdyz5wwjp4grys61mxb2ia9fi6i3ax6s43l16xnv291bxk7hld0"))))
  93     (build-system cmake-build-system)
  94     (inputs
  95      `(;; Our ICU is too recent: “error: ‘UChar’ does not name a type“.
  96        ;; ("icu4c" ,icu4c)
  97        ("libjpeg" ,libjpeg-turbo)
  98        ("libpng" ,libpng)
  99        ("libtiff" ,libtiff)
 100        ("libxml2" ,libxml2)
 101        ("openssl" ,openssl)
 102        ("zlib" ,zlib)))
 103     (native-inputs
 104      `(("doxygen" ,doxygen)))           ; for HTML documentation
 105     (home-page "https://dcmtk.org")
 106     (synopsis "Libraries and programs implementing parts of the DICOM standard")
 107     (description "DCMTK is a collection of libraries and applications
 108 implementing large parts the DICOM standard.  It includes software for
 109 examining, constructing and converting DICOM image files, handling offline
 110 media, sending and receiving images over a network connection, as well as
 111 demonstrative image storage and worklist servers.")
 112     (license (license:fsf-free
 113               "file://COPYRIGHT"
 114               "A union of the Apache 2.0 licence and various non-copyleft
 115 licences similar to the Modified BSD licence."))))
 116
 117 (define-public mia
 118   (package
 119     (name "mia")
 120     (version "2.4.6")
 121     (source (origin
 122               (method url-fetch)
 123               (uri (string-append "mirror://sourceforge/mia/mia/"
 124                                   (version-major+minor version)
 125                                   "/mia-" version ".tar.xz"))
 126               (sha256
 127                (base32
 128                 "0j4nd5z7i3v199jh7hqqhwd4g7snchizkc7rhzanpvngqg91m1pb"))))
 129     (build-system cmake-build-system)
 130     (arguments
 131      `(#:configure-flags
 132        (list "-DMIA_CREATE_NIPYPE_INTERFACES=0"
 133              "-DCMAKE_CXX_FLAGS=-fpermissive")))
 134     (inputs
 135      `(("boost" ,boost)
 136        ("dcmtk" ,dcmtk)
 137        ("doxygen" ,doxygen)
 138        ("eigen" ,eigen)
 139        ("fftw" ,fftw)
 140        ("fftwf" ,fftwf)
 141        ("gsl" ,gsl)
 142        ("gts" ,gts)
 143        ("hdf5" ,hdf5)
 144        ("itpp" ,itpp)
 145        ("libjpeg" ,libjpeg-turbo)
 146        ("libpng" ,libpng)
 147        ("libtiff" ,libtiff)
 148        ("libxml" ,libxml2)
 149        ("libxml++" ,libxml++)
 150        ("maxflow" ,maxflow)
 151        ("niftilib" ,niftilib)
 152        ("nlopt" ,nlopt)
 153        ("openexr" ,openexr)
 154        ("python-lxml" ,python2-lxml)
 155        ("vtk" ,vtk)))
 156     (native-inputs
 157      `(("pkg-config" ,pkg-config)
 158        ("python" ,python-2)))
 159     (home-page "http://mia.sourceforge.net")
 160     (synopsis "Toolkit for gray scale medical image analysis")
 161     (description "MIA provides a combination of command line tools, plug-ins,
 162 and libraries that make it possible run image processing tasks interactively
 163 in a command shell and to prototype using the shell's scripting language.  It
 164 is built around a plug-in structure that makes it easy to add functionality
 165 without compromising the original code base and it makes use of a wide variety
 166 of external libraries that provide additional functionality.")
 167     (license license:gpl3+)))
 168
 169 (define-public opencolorio
 170   (package
 171     (name "opencolorio")
 172     (version "1.1.1")
 173     (source
 174      (origin
 175        (method git-fetch)
 176        (uri (git-reference
 177              (url "https://github.com/AcademySoftwareFoundation/OpenColorIO")
 178              (commit (string-append "v" version))))
 179        (sha256
 180         (base32 "12srvxca51czpfjl0gabpidj9n84mw78ivxy5w75qhq2mmc798sb"))
 181        (file-name (git-file-name name version))
 182        (modules '((guix build utils)))
 183        (snippet
 184         `(begin
 185            ;; Remove bundled tarballs, patches, and .jars(!).  XXX: Upstream
 186            ;; claims to have fixed USE_EXTERNAL_YAML, but it still fails with:
 187            ;; https://github.com/AcademySoftwareFoundation/OpenColorIO/issues/517
 188            ;; When removing it, also remove it from the licence field comment.
 189            (for-each delete-file-recursively
 190                      (filter
 191                       (lambda (full-name)
 192                         (let ((file (basename full-name)))
 193                           (not (or (string-prefix? "yaml-cpp-0.3" file)
 194                                    (string=? "unittest.h" file)))))
 195                       (find-files "ext" ".*")))
 196
 197            #t))))
 198     (build-system cmake-build-system)
 199     (arguments
 200      `(#:configure-flags
 201        (list (string-append "-DCMAKE_CXX_FLAGS="
 202                             "-Wno-error=deprecated-declarations "
 203                             "-Wno-error=unused-function")
 204              "-DOCIO_BUILD_STATIC=OFF"
 205              ;; "-DUSE_EXTERNAL_YAML=ON"
 206              "-DUSE_EXTERNAL_TINYXML=ON"
 207              "-DUSE_EXTERNAL_LCMS=ON")
 208        #:phases
 209        (modify-phases %standard-phases
 210          (add-after 'unpack 'patch-test-suite
 211            (lambda _
 212              (substitute* "src/core_tests/CMakeLists.txt"
 213                (("/bin/sh") (which "bash")))
 214              #t)))))
 215     (native-inputs
 216      `(("git" ,git)
 217        ("pkg-config" ,pkg-config)))
 218     (inputs
 219      ;; XXX Adding freeglut, glew, ilmbase, mesa, and openimageio for
 220      ;; ocioconvert fails: error: conflicting declaration ?typedef void
 221      ;; (* PFNGLGETFRAGMENTMATERIALFVSGIXPROC)(GLenum, GLenum, GLfloat*)
 222      `(("lcms" ,lcms)
 223        ("openexr" ,openexr)
 224        ("tinyxml" ,tinyxml)))
 225     (home-page "https://opencolorio.org")
 226     (synopsis "Color management for visual effects and animation")
 227     (description
 228      "OpenColorIO, or OCIO, is a complete color management solution geared
 229 towards motion picture production, with an emphasis on visual effects and
 230 computer animation.  It provides a straightforward and consistent user
 231 experience across all supporting applications while allowing for sophisticated
 232 back-end configuration options suitable for high-end production usage.
 233
 234 OCIO is compatible with the @acronym{ACES, Academy Color Encoding
 235 Specification} and is @acronym{LUT, look-up table}-format agnostic, supporting
 236 many popular formats.")
 237     (license (list license:expat        ; docs/ociotheme/static, ext/yaml-cpp-*
 238                    license:zlib         ; src/core/md5
 239                    license:bsd-3))))    ; the rest
 240
 241 (define-public vtk
 242   (package
 243     (name "vtk")
 244     (version "8.2.0")
 245     (source (origin
 246               (method url-fetch)
 247               (uri (string-append "https://vtk.org/files/release/"
 248                                   (version-major+minor version)
 249                                   "/VTK-" version ".tar.gz"))
 250               (sha256
 251                (base32
 252                 "1fspgp8k0myr6p2a6wkc21ldcswb4bvmb484m12mxgk1a9vxrhrl"))))
 253     (build-system cmake-build-system)
 254     (arguments
 255      '(#:build-type "Release"           ;Build without '-g' to save space.
 256        ;; -DVTK_USE_SYSTEM_NETCDF:BOOL=TRUE requires netcdf_cxx
 257        #:configure-flags '("-DVTK_USE_SYSTEM_EXPAT:BOOL=TRUE"
 258                            "-DVTK_USE_SYSTEM_FREETYPE:BOOL=TRUE"
 259                            "-DVTK_USE_SYSTEM_HDF5:BOOL=TRUE"
 260                            "-DVTK_USE_SYSTEM_JPEG:BOOL=TRUE"
 261                            "-DVTK_USE_SYSTEM_JSONCPP:BOOL=TRUE"
 262                            "-DVTK_USE_SYSTEM_LIBXML2:BOOL=TRUE"
 263                            "-DVTK_USE_SYSTEM_OGGTHEORA:BOOL=TRUE"
 264                            "-DVTK_USE_SYSTEM_PNG:BOOL=TRUE"
 265                            "-DVTK_USE_SYSTEM_TIFF:BOOL=TRUE"
 266                            "-DVTK_USE_SYSTEM_ZLIB:BOOL=TRUE")
 267        #:tests? #f))                              ;XXX: no "test" target
 268     (inputs
 269      `(("libXt" ,libxt)
 270        ("xorgproto" ,xorgproto)
 271        ("libX11" ,libx11)
 272        ("libxml2" ,libxml2)
 273        ("mesa" ,mesa)
 274        ("glu" ,glu)
 275        ("expat" ,expat)
 276        ("freetype" ,freetype)
 277        ("hdf5" ,hdf5)
 278        ("jpeg" ,libjpeg-turbo)
 279        ("jsoncpp" ,jsoncpp)
 280        ("libogg" ,libogg)
 281        ("libtheora" ,libtheora)
 282        ("png" ,libpng)
 283        ("tiff" ,libtiff)
 284        ("zlib" ,zlib)))
 285     (home-page "https://vtk.org/")
 286     (synopsis "Libraries for 3D computer graphics")
 287     (description
 288      "The Visualization Toolkit (VTK) is a C++ library for 3D computer graphics,
 289 image processing and visualization.  It supports a wide variety of
 290 visualization algorithms including: scalar, vector, tensor, texture, and
 291 volumetric methods; and advanced modeling techniques such as: implicit
 292 modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay
 293 triangulation.  VTK has an extensive information visualization framework, has
 294 a suite of 3D interaction widgets, supports parallel processing, and
 295 integrates with various databases on GUI toolkits such as Qt and Tk.")
 296     (license license:bsd-3)))
 297
 298 ;; itksnap needs an older variant of VTK.
 299 (define-public vtk-6
 300   (package (inherit vtk)
 301     (version "6.3.0")
 302     (source (origin
 303               (method url-fetch)
 304               (uri (string-append "https://vtk.org/files/release/"
 305                                   (version-major+minor version)
 306                                   "/VTK-" version ".tar.gz"))
 307               (sha256
 308                (base32
 309                 "0pla1r5mvkgl4sl213gfdhzrypdgai0h3z5mfgm6p9jz9hsr794j"))))
 310     (inputs
 311      `(("jsoncpp" ,jsoncpp-for-tensorflow)
 312        ,@(alist-delete "jsoncpp" (package-inputs vtk))))))
 313
 314 (define-public opencv
 315   (package
 316     (name "opencv")
 317     (version "3.4.3")
 318     (source (origin
 319               (method git-fetch)
 320               (uri (git-reference
 321                      (url "https://github.com/opencv/opencv")
 322                      (commit version)))
 323               (file-name (git-file-name name version))
 324               (sha256
 325                (base32
 326                 "06bc61r8myym4s8im10brdjfg4wxkrvsbhhl7vr1msdan2xddzi3"))
 327               (patches
 328                (search-patches "opencv-fix-build-of-grfmt_jpeg2000.cpp.patch"))
 329               (modules '((guix build utils)))
 330               (snippet
 331                '(begin
 332                   ;; Remove external libraries. We have all available in Guix:
 333                   (delete-file-recursively "3rdparty")
 334
 335                   ;; Milky icon set is non-free:
 336                   (delete-file-recursively "modules/highgui/src/files_Qt/Milky")
 337
 338                   ;; Some jars found:
 339                   (for-each delete-file
 340                             '("modules/java/test/pure_test/lib/junit-4.11.jar"
 341                               "samples/java/sbt/sbt/sbt-launch.jar"))
 342                   #t))))
 343     (build-system cmake-build-system)
 344     (arguments
 345      `(#:configure-flags
 346        (list "-DWITH_IPP=OFF"
 347              "-DWITH_ITT=OFF"
 348              "-DWITH_CAROTENE=OFF" ; only visible on arm/aarch64
 349              "-DENABLE_PRECOMPILED_HEADERS=OFF"
 350
 351              ;; CPU-Features:
 352              ;; See cmake/OpenCVCompilerOptimizations.cmake
 353              ;; (CPU_ALL_OPTIMIZATIONS) for a list of all optimizations
 354              ;; BASELINE is the minimum optimization all CPUs must support
 355              ;;
 356              ;; DISPATCH is the list of optional dispatches.
 357              "-DCPU_BASELINE=SSE2"
 358
 359              ,@(match (%current-system)
 360                  ("x86_64-linux"
 361                   '("-DCPU_DISPATCH=NEON;VFPV3;FP16;SSE;SSE2;SSE3;SSSE3;SSE4_1;SSE4_2;POPCNT;AVX;FP16;AVX2;FMA3;AVX_512F;AVX512_SKX"
 362                     "-DCPU_DISPATCH_REQUIRE=SSE3,SSSE3,SSE4_1,SSE4_2,AVX,AVX2"))
 363                  ("armhf-linux"
 364                   '("-DCPU_BASELINE_DISABLE=NEON")) ; causes build failures
 365                  ("aarch64-linux"
 366                   '("-DCPU_BASELINE=NEON"
 367                     "-DCPU_DISPATCH=NEON;VFPV3;FP16"))
 368                  (_ '()))
 369
 370              "-DBUILD_PERF_TESTS=OFF"
 371              "-DBUILD_TESTS=ON"
 372
 373              (string-append "-DOPENCV_EXTRA_MODULES_PATH=" (getcwd)
 374                             "/opencv-contrib/modules")
 375
 376              ;;Define test data:
 377              (string-append "-DOPENCV_TEST_DATA_PATH=" (getcwd)
 378                             "/opencv-extra/testdata")
 379
 380              ;; Is ON by default and would try to rebuild 3rd-party protobuf,
 381              ;; which we had removed, which would lead to an error:
 382              "-DBUILD_PROTOBUF=OFF"
 383
 384              ;; Rebuild protobuf files, because we have a slightly different
 385              ;; version than the included one. If we would not update, we
 386              ;; would get a compile error later:
 387              "-DPROTOBUF_UPDATE_FILES=ON"
 388
 389              ;; xfeatures2d disabled, because it downloads extra binaries from
 390              ;; https://github.com/opencv/opencv_3rdparty
 391              ;; defined in xfeatures2d/cmake/download_{vgg|bootdesc}.cmake
 392              ;; Cmp this bug entry:
 393              ;; https://github.com/opencv/opencv_contrib/issues/1131
 394              "-DBUILD_opencv_xfeatures2d=OFF")
 395        #:phases
 396        (modify-phases %standard-phases
 397          (add-after 'unpack 'disable-broken-tests
 398            (lambda _
 399              ;; These tests fails with:
 400              ;; vtkXOpenGLRenderWindow (0x723990): Could not find a decent config
 401              ;; I think we have no OpenGL support with the Xvfb.
 402              (substitute* '("modules/viz/test/test_tutorial3.cpp"
 403                             "modules/viz/test/test_main.cpp"
 404                             "modules/viz/test/tests_simple.cpp"
 405                             "modules/viz/test/test_viz3d.cpp")
 406                (("(TEST\\(Viz, )([a-z].*\\).*)" all pre post)
 407                 (string-append pre "DISABLED_" post)))
 408
 409              ;; This one fails with "unknown file: Failure"
 410              ;; But I couldn't figure out which file was missing:
 411              (substitute* "../opencv-contrib/modules/face/test/test_face_align.cpp"
 412                (("(TEST\\(CV_Face_FacemarkKazemi, )(can_detect_landmarks\\).*)"
 413                  all pre post)
 414                 (string-append pre "DISABLED_" post)))
 415
 416              ;; Failure reason: Bad accuracy
 417              ;; Incorrect count of accurate poses [2nd case]: 90.000000 / 94.000000
 418              (substitute* "../opencv-contrib/modules/rgbd/test/test_odometry.cpp"
 419                (("(TEST\\(RGBD_Odometry_Rgbd, )(algorithmic\\).*)" all pre post)
 420                 (string-append pre "DISABLED_" post)))
 421              #t))
 422
 423          (add-after 'unpack 'unpack-submodule-sources
 424            (lambda* (#:key inputs #:allow-other-keys)
 425              (mkdir "../opencv-extra")
 426              (mkdir "../opencv-contrib")
 427              (copy-recursively (assoc-ref inputs "opencv-extra")
 428                                "../opencv-extra")
 429              (invoke "tar" "xvf"
 430                      (assoc-ref inputs "opencv-contrib")
 431                      "--strip-components=1"
 432                      "-C" "../opencv-contrib")))
 433
 434          (add-after 'set-paths 'add-ilmbase-include-path
 435            (lambda* (#:key inputs #:allow-other-keys)
 436            ;; OpenEXR propagates ilmbase, but its include files do not appear
 437            ;; in the CPATH, so we need to add "$ilmbase/include/OpenEXR/" to
 438            ;; the CPATH to satisfy the dependency on "ImathVec.h".
 439            (setenv "CPATH"
 440                    (string-append (assoc-ref inputs "ilmbase")
 441                                   "/include/OpenEXR"
 442                                   ":" (or (getenv "CPATH") "")))
 443            #t))
 444        (add-before 'check 'start-xserver
 445          (lambda* (#:key inputs #:allow-other-keys)
 446            (let ((xorg-server (assoc-ref inputs "xorg-server"))
 447                  (disp ":1"))
 448              (setenv "HOME" (getcwd))
 449              (setenv "DISPLAY" disp)
 450              ;; There must be a running X server and make check doesn't start one.
 451              ;; Therefore we must do it.
 452              (zero? (system (format #f "~a/bin/Xvfb ~a &" xorg-server disp)))))))))
 453     (native-inputs
 454      `(("pkg-config" ,pkg-config)
 455        ("xorg-server" ,xorg-server-for-tests) ; For running the tests
 456        ("opencv-extra"
 457         ,(origin
 458            (method git-fetch)
 459            (uri (git-reference
 460                   (url "https://github.com/opencv/opencv_extra")
 461                   (commit version)))
 462            (file-name (git-file-name "opencv_extra" version))
 463            (sha256
 464             (base32 "08p5xnq8n1jw8svvz0fnirfg7q8dm3p4a5dl7527s5xj0f9qn7lp"))))
 465        ("opencv-contrib"
 466         ,(origin
 467            (method git-fetch)
 468            (uri (git-reference
 469                   (url "https://github.com/opencv/opencv_contrib")
 470                   (commit version)))
 471            (file-name (git-file-name "opencv_contrib" version))
 472            (patches (search-patches "opencv-rgbd-aarch64-test-fix.patch"))
 473            (sha256
 474             (base32 "1f334glf39nk42mpqq6j732h3ql2mpz89jd4mcl678s8n73nfjh2"))))))
 475     (inputs `(("libjpeg" ,libjpeg-turbo)
 476               ("libpng" ,libpng)
 477               ("jasper" ,jasper)
 478               ;; ffmpeg 4.0 causes core dumps in tests.
 479               ("ffmpeg" ,ffmpeg-3.4)
 480               ("libtiff" ,libtiff)
 481               ("hdf5" ,hdf5)
 482               ("libgphoto2" ,libgphoto2)
 483               ("libwebp" ,libwebp)
 484               ("zlib" ,zlib)
 485               ("gtkglext" ,gtkglext)
 486               ("openexr" ,openexr)
 487               ("ilmbase" ,ilmbase)
 488               ("gtk+" ,gtk+-2)
 489               ("python-numpy" ,python-numpy)
 490               ("protobuf" ,protobuf)
 491               ("vtk" ,vtk)
 492               ("python" ,python)))
 493     ;; These three CVEs are not a problem of OpenCV, see:
 494     ;; https://github.com/opencv/opencv/issues/10998
 495     (properties '((lint-hidden-cve . ("CVE-2018-7712"
 496                                       "CVE-2018-7713"
 497                                       "CVE-2018-7714"))))
 498     (synopsis "Computer vision library")
 499     (description "OpenCV is a library aimed at
 500 real-time computer vision, including several hundred computer
 501 vision algorithms.  It can be used to do things like:
 502
 503 @itemize
 504 @item image and video input and output
 505 @item image and video processing
 506 @item displaying
 507 @item feature recognition
 508 @item segmentation
 509 @item facial recognition
 510 @item stereo vision
 511 @item structure from motion
 512 @item augmented reality
 513 @item machine learning
 514 @end itemize\n")
 515     (home-page "https://opencv.org/")
 516     (license license:bsd-3)))
 517
 518 (define-public vips
 519   (package
 520     (name "vips")
 521     (version "8.7.4")
 522     (source
 523      (origin
 524        (method url-fetch)
 525        (uri (string-append
 526              "https://github.com/libvips/libvips/releases/download/v"
 527              version "/vips-" version ".tar.gz"))
 528        (sha256
 529         (base32 "01gjhcrl6zj7mcj1al717v5jsniahplqhz1xkfh2j78vyfl1hxff"))))
 530     (build-system gnu-build-system)
 531     (native-inputs
 532      `(("pkg-config" ,pkg-config)
 533        ("gobject-introspection" ,gobject-introspection)))
 534     (inputs
 535      `(("glib" ,glib)
 536        ("libjpeg" ,libjpeg-turbo)
 537        ("libpng" ,libpng)
 538        ("librsvg" ,librsvg)
 539        ("libtiff" ,libtiff)
 540        ("libexif" ,libexif)
 541        ("giflib" ,giflib)
 542        ("libgsf" ,libgsf)
 543        ("fftw" ,fftw)
 544        ("poppler" ,poppler)
 545        ("pango" ,pango)
 546        ("lcms" ,lcms)
 547        ("matio" ,matio)
 548        ("libwebp" ,libwebp)
 549        ("niftilib" ,niftilib)
 550        ("openexr" ,openexr)
 551        ("orc" ,orc)
 552        ("imagemagick" ,imagemagick)
 553        ("libxml2" ,libxml2)
 554        ("expat" ,expat)
 555        ("hdf5" ,hdf5)))
 556     (home-page "https://libvips.github.io/libvips/")
 557     (synopsis "Multithreaded image processing system with low memory needs")
 558     (description
 559      "VIPS is a demand-driven, horizontally threaded image processing library.
 560 It's particularly good at processing large images, working with colour,
 561 scientific analysis, and general research & development.
 562
 563 Compared to most image processing libraries VIPS needs little RAM and runs
 564 quickly, especially on machines with more than one CPU core.  This is primarily
 565 due to its architecture which automatically parallelises the image workflows.")
 566     (license license:lgpl2.1+)))
 567
 568 (define-public gmic
 569   (package
 570     (name "gmic")
 571     (version "2.9.2")
 572     (source
 573      (origin
 574        (method url-fetch)
 575        (uri (string-append "https://gmic.eu/files/source/gmic_"
 576                            version ".tar.gz"))
 577        (sha256
 578         (base32 "14acph914a8lp6qqfmp319ggqjg3i3hmalmnpk3mp07m7vpv2p9q"))))
 579     (build-system cmake-build-system)
 580     (arguments
 581      `(#:tests? #f))                    ;there are no tests
 582     (native-inputs
 583      `(("pkg-config" ,pkg-config)))
 584     (inputs
 585      `(("curl" ,curl)
 586        ("fftw" ,fftw)
 587        ("graphicsmagick" ,graphicsmagick)
 588        ("libjpeg-turbo" ,libjpeg-turbo)
 589        ("libpng" ,libpng)
 590        ("libtiff" ,libtiff)
 591        ("libx11" ,libx11)
 592        ;;("opencv" ,opencv) ;OpenCV is currently broken in the CI
 593        ("openexr" ,openexr)
 594        ("zlib" ,zlib)))
 595     (home-page "https://gmic.eu/")
 596     (synopsis "Full-featured framework for digital image processing")
 597     (description "G'MIC is a full-featured framework for digital image
 598 processing.  It provides several user interfaces to convert / manipulate
 599 / filter / visualize generic image datasets, ranging from 1D scalar
 600 signals to 3D+t sequences of multi-spectral volumetric images, hence
 601 including 2D color images.")
 602     ;; Dual-licensed, either license applies.
 603     (license (list license:cecill license:cecill-c))))
 604
 605 (define-public nip2
 606   (package
 607     (name "nip2")
 608     (version "8.7.1")
 609     (source
 610      (origin
 611        (method url-fetch)
 612        (uri (string-append "https://github.com/libvips/nip2/releases/download/v"
 613                            version "/nip2-" version ".tar.gz" ))
 614        (sha256
 615         (base32 "0l7n427njif53npqn02gfjjly8y3khbrkzqxp10j5vp9h97psgiw"))))
 616     (build-system gnu-build-system)
 617     (arguments
 618      `(#:phases
 619        (modify-phases %standard-phases
 620          ;; test_conv.ws keep failing so disabling for now.
 621          (add-after 'unpack 'disable-test-conv
 622            (lambda _
 623              (delete-file "test/workspaces/test_conv.ws")
 624              #t))
 625          (add-before 'check 'set-home
 626            (lambda _
 627              (setenv "HOME" "/tmp") #t)))))
 628     (inputs
 629      `(("vips" ,vips)
 630        ("glib" ,glib)
 631        ("libtiff" ,libtiff)
 632        ("gtk+-2" ,gtk+-2)
 633        ("libxml2" ,libxml2)
 634        ("libexif" ,libexif)
 635        ("libjpeg" ,libjpeg-turbo)        ;required by vips.pc
 636        ("librsvg" ,librsvg)
 637        ("fftw" ,fftw)
 638        ("libgsf" ,libgsf)
 639        ("imagemagick" ,imagemagick)
 640        ("orc" ,orc)
 641        ("matio" ,matio)
 642        ("lcms" ,lcms)
 643        ("libwebp" ,libwebp)
 644        ("openexr" ,openexr)
 645        ("poppler" ,poppler)
 646        ("gsl" ,gsl)))
 647     (native-inputs
 648      `(("flex" ,flex)
 649        ("bison" ,bison)
 650        ("pkg-config" ,pkg-config)))
 651     (home-page "https://github.com/libvips/nip2")
 652     (synopsis "Spreadsheet-like GUI for libvips")
 653     (description "This package provide a graphical user interface (GUI) for
 654 the VIPS image processing library.  It's a little like a spreadsheet: you
 655 create a set of formula connecting your objects together, and on a change nip2
 656 recalculates.")
 657     (license license:gpl2+)))
 658
 659 (define-public vxl
 660   (package
 661     (name "vxl")
 662     (version "2.0.2")
 663     (source
 664      (origin
 665        (method git-fetch)
 666        (uri (git-reference
 667              (url "https://github.com/vxl/vxl")
 668              (commit (string-append "v" version))))
 669        (file-name (git-file-name name version))
 670        (sha256
 671         (base32 "0949hw57szq8943f1whwqaz591xjmb19kj803hcv74hdai2b0ycg"))
 672        (modules '((guix build utils)))
 673        ;; TODO: vxl includes an old version of dcmtk.  It won't build with
 674        ;; version 3.6.x.
 675        (snippet
 676         '(begin
 677            (for-each delete-file-recursively
 678                      '("v3p/bzlib/"
 679                        "v3p/geotiff/"
 680                        "v3p/jpeg/"
 681                        "v3p/png/"
 682                        "v3p/tiff/"
 683                        "v3p/zlib/"))
 684            (substitute* "v3p/CMakeLists.txt"
 685              (("add_subdirectory\\((tiff|png|jpeg|zlib|bzlib|geotiff)\\)")
 686               ""))
 687            #t))))
 688     (build-system cmake-build-system)
 689     (inputs
 690      `(("libgeotiff" ,libgeotiff)
 691        ("libtiff" ,libtiff)
 692        ("libjpeg" ,libjpeg-turbo)
 693        ("libpng" ,libpng)
 694        ("zlib" ,zlib)))
 695     (home-page "https://github.com/vxl/vxl/")
 696     (synopsis "Collection of C++ libraries for computer vision")
 697     (description "VXL (the Vision-something-Libraries) is a collection of C++
 698 libraries designed for computer vision research and implementation.")
 699     (license license:bsd-3)))
 700
 701 (define-public vxl-1
 702   (package (inherit vxl)
 703     (name "vxl")
 704     (version "1.18.0")
 705     (source
 706      (origin
 707        (method git-fetch)
 708        (uri (git-reference
 709              (url "https://github.com/vxl/vxl")
 710              (commit (string-append "v" version))))
 711        (file-name (git-file-name name version))
 712        (sha256
 713         (base32 "1g4mr2cc58jwm0vasscbd4y5380wj3ahkvq121z4gs83fhavvxgz"))
 714        (modules '((guix build utils)))
 715        (snippet
 716         '(begin
 717            (for-each delete-file-recursively
 718                      '("v3p/bzlib/"
 719                        "v3p/geotiff/"
 720                        "v3p/png/"
 721                        "v3p/tiff/"
 722                        "v3p/zlib/"))
 723            (substitute* "v3p/CMakeLists.txt"
 724              (("add_subdirectory\\((tiff|png|jpeg|zlib|bzlib|geotiff)\\)")
 725               ""))
 726            #t))))
 727     (arguments
 728      `(#:configure-flags
 729        ;; Needed for itk-snap
 730        (list "-DVNL_CONFIG_LEGACY_METHODS=ON")))))
 731
 732 (define-public insight-toolkit
 733   (package
 734     (name "insight-toolkit")
 735     (version "5.0.0")
 736     (source
 737      (origin
 738        (method url-fetch)
 739        (uri (string-append "https://github.com/InsightSoftwareConsortium/ITK/"
 740                            "releases/download/v" version "/InsightToolkit-"
 741                            version ".tar.xz"))
 742        (sha256
 743         (base32 "0bs63mk4q8jmx38f031jy5w5n9yy5ng9x8ijwinvjyvas8cichqi"))))
 744     (build-system cmake-build-system)
 745     (arguments
 746      `(#:tests? #f            ; tests require network access and external data
 747        #:configure-flags
 748        '("-DITK_USE_GPU=ON"
 749          "-DITK_USE_SYSTEM_LIBRARIES=ON"
 750          "-DITK_USE_SYSTEM_GOOGLETEST=ON"
 751          "-DITK_BUILD_SHARED=ON"
 752          ;; This prevents "GTest::GTest" from being added to the ITK_LIBRARIES
 753          ;; variable in the installed CMake files.  This is necessary as other
 754          ;; packages using insight-toolkit could not be configured otherwise.
 755          "-DGTEST_ROOT=gtest")
 756        #:phases
 757        (modify-phases %standard-phases
 758          (add-after 'unpack 'do-not-tune
 759            (lambda _
 760              (substitute* "CMake/ITKSetStandardCompilerFlags.cmake"
 761                (("-mute=native") ""))
 762              #t)))))
 763     (inputs
 764      `(("eigen" ,eigen)
 765        ("expat" ,expat)
 766        ("fftw" ,fftw)
 767        ("fftwf" ,fftwf)
 768        ("hdf5" ,hdf5)
 769        ("libjpeg" ,libjpeg-turbo)
 770        ("libpng" ,libpng)
 771        ("libtiff" ,libtiff)
 772        ("mesa" ,mesa-opencl)
 773        ("perl" ,perl)
 774        ("python" ,python)
 775        ("tbb" ,tbb)
 776        ("vxl" ,vxl-1)
 777        ("zlib" ,zlib)))
 778     (native-inputs
 779      `(("googletest" ,googletest)
 780        ("pkg-config" ,pkg-config)))
 781     (home-page "https://github.com/InsightSoftwareConsortium/ITK/")
 782     (synopsis "Scientific image processing, segmentation and registration")
 783     (description "The Insight Toolkit (ITK) is a toolkit for N-dimensional
 784 scientific image processing, segmentation, and registration.  Segmentation is
 785 the process of identifying and classifying data found in a digitally sampled
 786 representation.  Typically the sampled representation is an image acquired
 787 from such medical instrumentation as CT or MRI scanners.  Registration is the
 788 task of aligning or developing correspondences between data.  For example, in
 789 the medical environment, a CT scan may be aligned with a MRI scan in order to
 790 combine the information contained in both.")
 791     (license license:asl2.0)))
 792
 793 (define-public insight-toolkit-4
 794   (package (inherit insight-toolkit)
 795     (version "4.13.2")
 796     (source
 797      (origin
 798        (method url-fetch)
 799        (uri (string-append "https://github.com/InsightSoftwareConsortium/ITK/"
 800                            "releases/download/v" version "/InsightToolkit-"
 801                            version ".tar.xz"))
 802        (sha256
 803         (base32 "19cgfpd63gqrvc3m27m394gy2d7w79g5y6lvznb5qqr49lihbgns"))))
 804     (arguments
 805      `(#:tests? #f            ; tests require network access and external data
 806        #:configure-flags
 807        '("-DITKV3_COMPATIBILITY=ON"     ; needed for itk-snap
 808          "-DITK_USE_GPU=ON"
 809          "-DITK_USE_SYSTEM_LIBRARIES=ON"
 810          "-DITK_USE_SYSTEM_GOOGLETEST=ON"
 811          "-DITK_USE_SYSTEM_VXL=ON")))))
 812
 813 (define-public insight-toolkit-4.12
 814   (package (inherit insight-toolkit-4)
 815     (version "4.12.2")
 816     (source
 817      (origin
 818        (method url-fetch)
 819        (uri (string-append "mirror://sourceforge/itk/itk/4.12/"
 820                            "InsightToolkit-" version ".tar.xz"))
 821        (sha256
 822         (base32 "1qw9mxbh083siljygahl4gdfv91xvfd8hfl7ghwii19f60xrvn2w"))))))
 823
 824 (define-public itk-snap
 825   (package
 826     (name "itk-snap")
 827     (version "3.8.0")
 828     (source
 829      (origin
 830        (method git-fetch)
 831        (uri (git-reference
 832              (url "https://git.code.sf.net/p/itk-snap/src")
 833              (commit (string-append "v" version))))
 834        (file-name (git-file-name name version))
 835        (sha256
 836         (base32 "15i5ixpryfrbf3vrrb5rici8fb585f25k0v1ljds16bp1f1msr4q"))))
 837     (build-system cmake-build-system)
 838     (arguments
 839      `(#:configure-flags
 840        (list "-DSNAP_VERSION_GIT_SHA1=release"
 841              "-DSNAP_VERSION_GIT_BRANCH=release"
 842              "-DSNAP_VERSION_GIT_TIMESTAMP=0"
 843              "-DSNAP_PACKAGE_QT_PLUGINS=OFF"
 844              "-DCMAKE_POSITION_INDEPENDENT_CODE=ON")
 845        #:phases
 846        (modify-phases %standard-phases
 847          ;; During the installation phase all libraries provided by all
 848          ;; dependencies will be copied to the lib directory.  That's insane,
 849          ;; so we disable this.
 850          (add-after 'unpack 'do-not-copy-dependencies
 851            (lambda _
 852              (substitute* "CMakeLists.txt"
 853                (("install_qt5_executable\
 854 \\(\\$\\{SNAP_MAIN_INSTALL_DIR\\}/\\$\\{SNAP_EXE\\}\\)")
 855                 ""))
 856              #t))
 857          (add-after 'unpack 'disable-gui-tests
 858            (lambda _
 859              ;; The GUI tests just time out.
 860              (substitute* "CMakeLists.txt"
 861                (("  (Workspace|DiffSpace|ProbeIntensity|RegionCompetition\
 862 |RandomForest|RandomForestBailOut)")
 863                 ""))
 864              #t))
 865          (add-after 'unpack 'make-reproducible
 866            (lambda _
 867              (substitute* "CMakeLists.txt"
 868                (("TODAY\\(SNAP_VERSION_COMPILE_DATE\\)")
 869                 "SET(SNAP_VERSION_COMPILE_DATE \"(removed for reproducibility)\")"))
 870              #t))
 871          (add-after 'unpack 'prepare-submodules
 872            (lambda* (#:key inputs #:allow-other-keys)
 873              (rmdir "Submodules/c3d")
 874              (copy-recursively (assoc-ref inputs "c3d-src")
 875                                "Submodules/c3d")
 876              (substitute* '("Submodules/c3d/adapters/BiasFieldCorrectionN4.cxx"
 877                             "Submodules/c3d/adapters/ApplyMetric.cxx")
 878                (("vcl_") "std::"))
 879              (rmdir "Submodules/greedy")
 880              (symlink (assoc-ref inputs "greedy-src")
 881                       "Submodules/greedy")
 882              #t))
 883          (add-after 'unpack 'fix-includes
 884            (lambda _
 885              (substitute* "GUI/Model/RegistrationModel.cxx"
 886                (("<vnl_symmetric_eigensystem.h>")
 887                 "<vnl/algo/vnl_symmetric_eigensystem.h>"))
 888              #t))
 889          (add-before 'check 'prepare-tests
 890            (lambda _
 891              ;; Needed by at least one test.
 892              (setenv "HOME" "/tmp")
 893              #t))
 894          (add-after 'install 'wrap-executable
 895            (lambda* (#:key inputs outputs #:allow-other-keys)
 896              (let ((out (assoc-ref outputs "out")))
 897                (wrap-program (string-append out "/bin/itksnap")
 898                  `("QT_PLUGIN_PATH" ":" prefix
 899                    ,(map (lambda (label)
 900                            (string-append (assoc-ref inputs label)
 901                                           "/lib/qt5/plugins"))
 902                          '("qtbase" "qtdeclarative"))))
 903                #t))))))
 904     (inputs
 905      `(("curl" ,curl)
 906        ("fftw" ,fftw)
 907        ("fftwf" ,fftwf)
 908        ("glu" ,glu)
 909        ("hdf5" ,hdf5)
 910        ("mesa" ,mesa-opencl)
 911        ;; This package does not build with either insight-toolkit 5.0.0 and
 912        ;; not with 4.13.  It really needs to be 4.12.
 913        ("itk" ,insight-toolkit-4.12)
 914        ("vtk" ,vtk-6)
 915        ("qtbase" ,qtbase)
 916        ("qtdeclarative" ,qtdeclarative)
 917        ("vxl" ,vxl-1)
 918        ("zlib" ,zlib)))
 919     (native-inputs
 920      `(("googletest" ,googletest)
 921        ("qttools" ,qttools)
 922        ("pkg-config" ,pkg-config)
 923        ("c3d-src"
 924         ,(let* ((commit "f521358db26e00002c911cc47bf463b043942ad3")
 925                 (revision "1")
 926                 (version (git-version "0" revision commit)))
 927            (origin
 928              (method git-fetch)
 929              (uri (git-reference
 930                    (url "https://github.com/pyushkevich/c3d")
 931                    (commit commit)))
 932              (file-name (git-file-name "c3d" version))
 933              (sha256
 934               (base32
 935                "0kyv3rxrxwr8c3sa9zv01lsnhk95b27gx1s870k3yi8qp52h7bx3")))))
 936        ;; We are using an arbitrary commit from 2017 because the latest
 937        ;; version breaks the build...
 938        ("greedy-src"
 939         ,(let* ((commit "97e340f7e8e66597599144947775e6039e79a0d3")
 940                 (revision "1")
 941                 (version (git-version "0" revision commit)))
 942            (origin
 943              (method git-fetch)
 944              (uri (git-reference
 945                    (url "https://github.com/pyushkevich/greedy")
 946                    (commit commit)))
 947              (file-name (git-file-name "greedy" version))
 948              (sha256
 949               (base32
 950                "0k5bc9za4jrc8z9dj08z1rkcp5xf0gnd1d2jmi1w9ny4vxh2q2ab")))))))
 951     (home-page "https://sourceforge.net/p/itk-snap/")
 952     (synopsis "Medical image segmentation")
 953     (description "ITK-SNAP is a tool for segmenting anatomical structures in
 954 medical images.  It provides an automatic active contour segmentation
 955 pipeline, along with supporting a manual segmentation toolbox.  ITK-SNAP has a
 956 full-featured UI aimed at clinical researchers.")
 957     ;; This includes the submodules greedy and c3d.
 958     (license license:gpl3+)))
 959
 960 (define-public metapixel
 961   ;; Follow stable branch.
 962   (let ((commit "98ee9daa093b6c334941242e63f90b1c2876eb4f"))
 963     (package
 964       (name "metapixel")
 965       (version (git-version "1.0.2" "1" commit))
 966       (source
 967        (origin
 968          (method git-fetch)
 969          (uri (git-reference
 970                (url "https://github.com/schani/metapixel")
 971                (commit commit)
 972                ;; TODO: Package rwimg and lispreader?
 973                (recursive? #t)))
 974          (file-name (git-file-name name version))
 975          (sha256
 976           (base32 "0r7n3a6bvcxkbpda4mwmrpicii09iql5z69nkjqygkwxw7ny3309"))))
 977       (build-system gnu-build-system)
 978       (inputs
 979        `(("giflib" ,giflib)
 980          ("libjpeg" ,libjpeg-turbo)
 981          ("libpng" ,libpng)
 982          ("perl" ,perl)))
 983       (native-inputs
 984        `(("pkg-config" ,pkg-config)
 985          ("docbook-xml" ,docbook-xml)
 986          ("docbook-xsl" ,docbook-xsl)
 987          ("xsltproc" ,libxslt)))
 988       (arguments
 989        `(#:tests? #f                    ; No tests.
 990          #:make-flags (list
 991                        (string-append "PREFIX=" (assoc-ref %outputs "out"))
 992                        (string-append "MANPAGE_XSL="
 993                                       (assoc-ref %build-inputs "docbook-xsl")
 994                                       "/xml/xsl/docbook-xsl-*/manpages/docbook.xsl"))
 995          #:phases
 996          (modify-phases %standard-phases
 997            (delete 'configure)
 998            (add-before 'install 'make-local-docbook-xml
 999              (lambda* (#:key inputs #:allow-other-keys)
1000                (substitute* "metapixel.xml"
1001                  (("http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd")
1002                   (string-append (assoc-ref inputs "docbook-xml")
1003                                  "/xml/dtd/docbook/docbookx.dtd")))
1004                #t))
1005            (add-before 'install 'fix-directory-creation
1006              (lambda* (#:key outputs #:allow-other-keys)
1007                (mkdir-p (string-append (assoc-ref outputs "out") "/share/man/man1"))
1008                #t)))))
1009       (home-page "https://www.complang.tuwien.ac.at/schani/metapixel/")
1010       (synopsis "Photomosaics generator")
1011       (description "Metapixel is a program for generating photomosaics.  It can
1012 generate classical photomosaics, in which the source image is viewed as a
1013 matrix of equally sized rectangles for each of which a matching image is
1014 substitued, as well as collage-style photomosaics, in which rectangular parts
1015 of the source image at arbitrary positions (i.e. not aligned to a matrix) are
1016 substituted by matching images.")
1017       (license license:gpl2))))