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, 2021 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 © 2018–2021 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, 2021 Efraim Flashner <efraim@flashner.co.il>
  11 ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
  12 ;;; Copyright © 2020, 2021 Vinicius Monego <monego@posteo.net>
  13 ;;; Copyright © 2020 Pierre Neidhardt <mail@ambrevar.xyz>
  14 ;;; Copyright © 2020 Brendan Tildesley <mail@brendan.scot>
  15 ;;; Copyright © 2021 Oleh Malyi <astroclubzp@gmail.com>
  16 ;;; Copyright © 2021 Felix Gruber <felgru@posteo.net>
  17 ;;; Copyright © 2021 Andy Tai <atai@atai.org>
  18 ;;; Copyright © 2021 Ekaitz Zarraga <ekaitz@elenq.tech>
  19 ;;;
  20 ;;; This file is part of GNU Guix.
  21 ;;;
  22 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  23 ;;; under the terms of the GNU General Public License as published by
  24 ;;; the Free Software Foundation; either version 3 of the License, or (at
  25 ;;; your option) any later version.
  26 ;;;
  27 ;;; GNU Guix is distributed in the hope that it will be useful, but
  28 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  29 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  30 ;;; GNU General Public License for more details.
  31 ;;;
  32 ;;; You should have received a copy of the GNU General Public License
  33 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  34
  35 (define-module (gnu packages image-processing)
  36   #:use-module ((guix licenses) #:prefix license:)
  37   #:use-module (guix packages)
  38   #:use-module (guix utils)
  39   #:use-module (guix download)
  40   #:use-module (guix git-download)
  41   #:use-module (guix build-system qt)
  42   #:use-module (guix build-system cmake)
  43   #:use-module (guix build-system gnu)
  44   #:use-module (gnu packages)
  45   #:use-module (gnu packages algebra)
  46   #:use-module (gnu packages bison)
  47   #:use-module (gnu packages boost)
  48   #:use-module (gnu packages check)
  49   #:use-module (gnu packages compression)
  50   #:use-module (gnu packages curl)
  51   #:use-module (gnu packages docbook)
  52   #:use-module (gnu packages documentation)
  53   #:use-module (gnu packages flex)
  54   #:use-module (gnu packages fontutils)
  55   #:use-module (gnu packages geo)
  56   #:use-module (gnu packages ghostscript)
  57   #:use-module (gnu packages gl)
  58   #:use-module (gnu packages glib)
  59   #:use-module (gnu packages gnome)
  60   #:use-module (gnu packages graphics)
  61   #:use-module (gnu packages graphviz)
  62   #:use-module (gnu packages gstreamer)
  63   #:use-module (gnu packages gtk)
  64   #:use-module (gnu packages icu4c)
  65   #:use-module (gnu packages image)
  66   #:use-module (gnu packages imagemagick)
  67   #:use-module (gnu packages maths)
  68   #:use-module (gnu packages pdf)
  69   #:use-module (gnu packages perl)
  70   #:use-module (gnu packages photo)
  71   #:use-module (gnu packages pkg-config)
  72   #:use-module (gnu packages protobuf)
  73   #:use-module (gnu packages python)
  74   #:use-module (gnu packages python-xyz)
  75   #:use-module (gnu packages qt)
  76   #:use-module (gnu packages serialization)
  77   #:use-module (gnu packages sqlite)
  78   #:use-module (gnu packages tbb)
  79   #:use-module (gnu packages tls)
  80   #:use-module (gnu packages version-control)
  81   #:use-module (gnu packages video)
  82   #:use-module (gnu packages xiph)
  83   #:use-module (gnu packages xml)
  84   #:use-module (gnu packages xorg)
  85   #:use-module (ice-9 match)
  86   #:use-module (srfi srfi-1))
  87
  88 (define-public dcmtk
  89   (package
  90     (name "dcmtk")
  91     (version "3.6.6")
  92     (source
  93      (origin
  94        (method url-fetch)
  95        (uri
  96         (string-append "ftp://dicom.offis.de/pub/dicom/offis/software/dcmtk/"
  97                        "dcmtk" (string-join (string-split version #\.) "")
  98                        "/dcmtk-" version ".tar.gz"))
  99        (sha256
 100         (base32 "13j5yf3p6qj3mr17d77r3kcqchf055hgvk1w15vmdr8f54mwcnb8"))))
 101     (build-system cmake-build-system)
 102     (inputs
 103      `(("icu4c" ,icu4c)
 104        ("libjpeg" ,libjpeg-turbo)
 105        ("libpng" ,libpng)
 106        ("libtiff" ,libtiff)
 107        ("libxml2" ,libxml2)
 108        ("openssl" ,openssl)
 109        ("zlib" ,zlib)))
 110     (native-inputs
 111      `(("doxygen" ,doxygen)))           ; for HTML documentation
 112     (home-page "https://dcmtk.org")
 113     (synopsis "Libraries and programs implementing parts of the DICOM standard")
 114     (description "DCMTK is a collection of libraries and applications
 115 implementing large parts the DICOM standard.  It includes software for
 116 examining, constructing and converting DICOM image files, handling offline
 117 media, sending and receiving images over a network connection, as well as
 118 demonstrative image storage and worklist servers.")
 119     (license (license:fsf-free
 120               "file://COPYRIGHT"
 121               "A union of the Apache 2.0 licence and various non-copyleft
 122 licences similar to the Modified BSD licence."))))
 123
 124 (define-public mia
 125   (package
 126     (name "mia")
 127     (version "2.4.6")
 128     (source (origin
 129               (method url-fetch)
 130               (uri (string-append "mirror://sourceforge/mia/mia/"
 131                                   (version-major+minor version)
 132                                   "/mia-" version ".tar.xz"))
 133               (sha256
 134                (base32
 135                 "0j4nd5z7i3v199jh7hqqhwd4g7snchizkc7rhzanpvngqg91m1pb"))))
 136     (build-system cmake-build-system)
 137     (arguments
 138      `(#:configure-flags
 139        (list "-DMIA_CREATE_NIPYPE_INTERFACES=0"
 140              "-DCMAKE_CXX_FLAGS=-fpermissive")))
 141     (inputs
 142      `(("boost" ,boost)
 143        ("dcmtk" ,dcmtk)
 144        ("doxygen" ,doxygen)
 145        ("eigen" ,eigen)
 146        ("fftw" ,fftw)
 147        ("fftwf" ,fftwf)
 148        ("gsl" ,gsl)
 149        ("gts" ,gts)
 150        ("hdf5" ,hdf5)
 151        ("itpp" ,itpp)
 152        ("libjpeg" ,libjpeg-turbo)
 153        ("libpng" ,libpng)
 154        ("libtiff" ,libtiff)
 155        ("libxml" ,libxml2)
 156        ("libxml++" ,libxml++)
 157        ("maxflow" ,maxflow)
 158        ("niftilib" ,niftilib)
 159        ("nlopt" ,nlopt)
 160        ("openexr" ,openexr)
 161        ("python-lxml" ,python2-lxml)
 162        ("vtk" ,vtk)))
 163     (native-inputs
 164      `(("pkg-config" ,pkg-config)
 165        ("python" ,python-2)))
 166     (home-page "http://mia.sourceforge.net")
 167     (synopsis "Toolkit for gray scale medical image analysis")
 168     (description "MIA provides a combination of command line tools, plug-ins,
 169 and libraries that make it possible run image processing tasks interactively
 170 in a command shell and to prototype using the shell's scripting language.  It
 171 is built around a plug-in structure that makes it easy to add functionality
 172 without compromising the original code base and it makes use of a wide variety
 173 of external libraries that provide additional functionality.")
 174     (license license:gpl3+)))
 175
 176 (define-public opencolorio
 177   (package
 178     (name "opencolorio")
 179     (version "1.1.1")
 180     (source
 181      (origin
 182        (method git-fetch)
 183        (uri (git-reference
 184              (url "https://github.com/AcademySoftwareFoundation/OpenColorIO")
 185              (commit (string-append "v" version))))
 186        (sha256
 187         (base32 "12srvxca51czpfjl0gabpidj9n84mw78ivxy5w75qhq2mmc798sb"))
 188        (file-name (git-file-name name version))
 189        (modules '((guix build utils)))
 190        (snippet
 191         `(begin
 192            ;; Remove bundled tarballs, patches, and .jars(!).  XXX: Upstream
 193            ;; claims to have fixed USE_EXTERNAL_YAML, but it still fails with:
 194            ;; https://github.com/AcademySoftwareFoundation/OpenColorIO/issues/517
 195            ;; When removing it, also remove it from the licence field comment.
 196            (for-each delete-file-recursively
 197                      (filter
 198                       (lambda (full-name)
 199                         (let ((file (basename full-name)))
 200                           (not (or (string-prefix? "yaml-cpp-0.3" file)
 201                                    (string=? "unittest.h" file)))))
 202                       (find-files "ext" ".*")))
 203
 204            #t))))
 205     (build-system cmake-build-system)
 206     (arguments
 207      `(#:configure-flags
 208        (list (string-append "-DCMAKE_CXX_FLAGS="
 209                             "-Wno-error=deprecated-declarations "
 210                             "-Wno-error=unused-function")
 211              "-DOCIO_BUILD_STATIC=OFF"
 212              ;; "-DUSE_EXTERNAL_YAML=ON"
 213              "-DUSE_EXTERNAL_TINYXML=ON"
 214              "-DUSE_EXTERNAL_LCMS=ON")
 215        #:phases
 216        (modify-phases %standard-phases
 217          (add-after 'unpack 'patch-test-suite
 218            (lambda _
 219              (substitute* "src/core_tests/CMakeLists.txt"
 220                (("/bin/sh") (which "bash")))
 221              #t)))))
 222     (native-inputs
 223      `(("git" ,git)
 224        ("pkg-config" ,pkg-config)))
 225     (inputs
 226      ;; XXX Adding freeglut, glew, ilmbase, mesa, and openimageio for
 227      ;; ocioconvert fails: error: conflicting declaration ?typedef void
 228      ;; (* PFNGLGETFRAGMENTMATERIALFVSGIXPROC)(GLenum, GLenum, GLfloat*)
 229      `(("lcms" ,lcms)
 230        ("openexr" ,openexr)
 231        ("tinyxml" ,tinyxml)))
 232     (home-page "https://opencolorio.org")
 233     (synopsis "Color management for visual effects and animation")
 234     (description
 235      "OpenColorIO, or OCIO, is a complete color management solution geared
 236 towards motion picture production, with an emphasis on visual effects and
 237 computer animation.  It provides a straightforward and consistent user
 238 experience across all supporting applications while allowing for sophisticated
 239 back-end configuration options suitable for high-end production usage.
 240
 241 OCIO is compatible with the @acronym{ACES, Academy Color Encoding
 242 Specification} and is @acronym{LUT, look-up table}-format agnostic, supporting
 243 many popular formats.")
 244     (license (list license:expat        ; docs/ociotheme/static, ext/yaml-cpp-*
 245                    license:zlib         ; src/core/md5
 246                    license:bsd-3))))    ; the rest
 247
 248 (define-public vtk
 249   (package
 250     (name "vtk")
 251     (version "9.0.1")
 252     (source (origin
 253               (method url-fetch)
 254               (uri (string-append "https://vtk.org/files/release/"
 255                                   (version-major+minor version)
 256                                   "/VTK-" version ".tar.gz"))
 257               (sha256
 258                (base32
 259                 "1ir2lq9i45ls374lcmjzw0nrm5l5hnm1w47lg8g8d0n2j7hsaf8v"))
 260               (patches
 261                (search-patches "vtk-fix-freetypetools-build-failure.patch"))
 262               (modules '((guix build utils)))
 263               (snippet
 264                '(begin
 265                   (for-each
 266                     (lambda (dir)
 267                       (delete-file-recursively
 268                         (string-append "ThirdParty/" dir "/vtk" dir)))
 269                     ;; pugixml depended upon unconditionally
 270                     '("doubleconversion" "eigen" "expat" "freetype" "gl2ps"
 271                       "glew" "hdf5" "jpeg" "jsoncpp" "libproj" "libxml2" "lz4"
 272                       "netcdf" "ogg" "png" "sqlite" "theora" "tiff" "zlib"))
 273                   #t))))
 274     (properties `((release-monitoring-url . "https://vtk.org/download/")))
 275     (build-system cmake-build-system)
 276     (arguments
 277      '(#:build-type "Release"           ;Build without '-g' to save space.
 278        #:configure-flags '(;"-DBUILD_TESTING:BOOL=TRUE"
 279                            ;    ; not honored
 280                            "-DVTK_USE_EXTERNAL=OFF" ;; default
 281                            "-DVTK_MODULE_USE_EXTERNAL_VTK_doubleconversion=ON"
 282                            "-DVTK_MODULE_USE_EXTERNAL_VTK_eigen=ON"
 283                            "-DVTK_MODULE_USE_EXTERNAL_VTK_expat=ON"
 284                            "-DVTK_MODULE_USE_EXTERNAL_VTK_freetype=ON"
 285                            "-DVTK_MODULE_USE_EXTERNAL_VTK_gl2ps=ON"
 286                            "-DVTK_MODULE_USE_EXTERNAL_VTK_glew=ON"
 287                            "-DVTK_MODULE_USE_EXTERNAL_VTK_hdf5=ON"
 288                            "-DVTK_MODULE_USE_EXTERNAL_VTK_jpeg=ON"
 289                            "-DVTK_MODULE_USE_EXTERNAL_VTK_jsoncpp=ON"
 290                            "-DVTK_MODULE_USE_EXTERNAL_VTK_libproj=ON"
 291                            "-DVTK_MODULE_USE_EXTERNAL_VTK_libxml2=ON"
 292                            "-DVTK_MODULE_USE_EXTERNAL_VTK_lz4=ON"
 293                            "-DVTK_MODULE_USE_EXTERNAL_VTK_netcdf=ON"
 294                            "-DVTK_MODULE_USE_EXTERNAL_VTK_ogg=ON"
 295                            "-DVTK_MODULE_USE_EXTERNAL_VTK_png=ON"
 296                            ;"-DVTK_MODULE_USE_EXTERNAL_VTK_pugixml=ON"    ; breaks IO/CityGML
 297                            "-DVTK_MODULE_USE_EXTERNAL_VTK_sqlite=ON"
 298                            "-DVTK_MODULE_USE_EXTERNAL_VTK_theora=ON"
 299                            "-DVTK_MODULE_USE_EXTERNAL_VTK_tiff=ON"
 300                            "-DVTK_MODULE_USE_EXTERNAL_VTK_zlib=ON"
 301                            )
 302        #:phases
 303          (modify-phases %standard-phases
 304            (add-after 'unpack 'patch-sources
 305              (lambda _
 306                (substitute* "Common/Core/vtkFloatingPointExceptions.cxx"
 307                  (("<fenv.h>") "<cfenv>"))
 308                (substitute* "Common/Core/CMakeLists.txt"
 309                  (("fenv.h") "cfenv")))))
 310        #:tests? #f))        ;XXX: test data not included
 311     (inputs
 312      `(("double-conversion" ,double-conversion)
 313        ("eigen" ,eigen)
 314        ("expat" ,expat)
 315        ("freetype" ,freetype)
 316        ("gl2ps" ,gl2ps)
 317        ("glew" ,glew)
 318        ("glu" ,glu)
 319        ("hdf5" ,hdf5)
 320        ("jpeg" ,libjpeg-turbo)
 321        ("jsoncpp" ,jsoncpp)
 322        ("libtheora" ,libtheora)
 323        ("libX11" ,libx11)
 324        ("libxml2" ,libxml2)
 325        ("libXt" ,libxt)
 326        ("lz4" ,lz4)
 327        ("mesa" ,mesa)
 328        ("netcdf" ,netcdf)
 329        ("png" ,libpng)
 330        ("proj" ,proj.4)
 331        ;("pugixml" ,pugixml)
 332        ("sqlite" ,sqlite)
 333        ("tiff" ,libtiff)
 334        ("xorgproto" ,xorgproto)
 335        ("zlib" ,zlib)))
 336     (propagated-inputs
 337      ;; VTK's 'VTK-vtk-module-find-packages.cmake' calls
 338      ;; 'find_package(THEORA)', which in turns looks for libogg.
 339      `(("libogg" ,libogg)))
 340     (home-page "https://vtk.org/")
 341     (synopsis "Libraries for 3D computer graphics")
 342     (description
 343      "The Visualization Toolkit (VTK) is a C++ library for 3D computer graphics,
 344 image processing and visualization.  It supports a wide variety of
 345 visualization algorithms including: scalar, vector, tensor, texture, and
 346 volumetric methods; and advanced modeling techniques such as: implicit
 347 modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay
 348 triangulation.  VTK has an extensive information visualization framework, has
 349 a suite of 3D interaction widgets, supports parallel processing, and
 350 integrates with various databases on GUI toolkits such as Qt and Tk.")
 351     (license license:bsd-3)))
 352
 353 ;; freecad needs an old version of VTK, because VTK's API changed from 8 to 9
 354 (define-public vtk-8
 355   (package (inherit vtk)
 356     (version "8.2.0")
 357     (source (origin
 358               (method url-fetch)
 359               (uri (string-append "https://vtk.org/files/release/"
 360                                   (version-major+minor version)
 361                                   "/VTK-" version ".tar.gz"))
 362               (sha256
 363                (base32
 364                 "1fspgp8k0myr6p2a6wkc21ldcswb4bvmb484m12mxgk1a9vxrhrl"))))
 365     (inputs
 366      `(("jsoncpp" ,jsoncpp-for-tensorflow)
 367        ,@(alist-delete "jsoncpp" (package-inputs vtk))))))
 368
 369 ;; itksnap needs an older variant of VTK.
 370 (define-public vtk-6
 371   (package (inherit vtk)
 372     (version "6.3.0")
 373     (source (origin
 374               (method url-fetch)
 375               (uri (string-append "https://vtk.org/files/release/"
 376                                   (version-major+minor version)
 377                                   "/VTK-" version ".tar.gz"))
 378               (sha256
 379                (base32
 380                 "0pla1r5mvkgl4sl213gfdhzrypdgai0h3z5mfgm6p9jz9hsr794j"))))
 381     (inputs
 382      `(("jsoncpp" ,jsoncpp-for-tensorflow)
 383        ,@(alist-delete "jsoncpp" (package-inputs vtk))))))
 384
 385 (define-public opencv
 386   (package
 387     (name "opencv")
 388     (version "3.4.3")
 389     (source (origin
 390               (method git-fetch)
 391               (uri (git-reference
 392                      (url "https://github.com/opencv/opencv")
 393                      (commit version)))
 394               (file-name (git-file-name name version))
 395               (sha256
 396                (base32
 397                 "06bc61r8myym4s8im10brdjfg4wxkrvsbhhl7vr1msdan2xddzi3"))
 398               (patches
 399                (search-patches "opencv-fix-build-of-grfmt_jpeg2000.cpp.patch"))
 400               (modules '((guix build utils)))
 401               (snippet
 402                '(begin
 403                   ;; Remove external libraries. We have all available in Guix:
 404                   (delete-file-recursively "3rdparty")
 405
 406                   ;; Milky icon set is non-free:
 407                   (delete-file-recursively "modules/highgui/src/files_Qt/Milky")
 408
 409                   ;; Some jars found:
 410                   (for-each delete-file
 411                             '("modules/java/test/pure_test/lib/junit-4.11.jar"
 412                               "samples/java/sbt/sbt/sbt-launch.jar"))
 413                   #t))))
 414     (build-system cmake-build-system)
 415     (arguments
 416      `(#:configure-flags
 417        (list "-DWITH_IPP=OFF"
 418              "-DWITH_ITT=OFF"
 419              "-DWITH_CAROTENE=OFF" ; only visible on arm/aarch64
 420              "-DENABLE_PRECOMPILED_HEADERS=OFF"
 421
 422              ;; CPU-Features:
 423              ;; See cmake/OpenCVCompilerOptimizations.cmake
 424              ;; (CPU_ALL_OPTIMIZATIONS) for a list of all optimizations
 425              ;; BASELINE is the minimum optimization all CPUs must support
 426              ;;
 427              ;; DISPATCH is the list of optional dispatches.
 428              "-DCPU_BASELINE=SSE2"
 429
 430              ,@(match (%current-system)
 431                  ("x86_64-linux"
 432                   '("-DCPU_DISPATCH=NEON;VFPV3;FP16;SSE;SSE2;SSE3;SSSE3;SSE4_1;SSE4_2;POPCNT;AVX;FP16;AVX2;FMA3;AVX_512F;AVX512_SKX"
 433                     "-DCPU_DISPATCH_REQUIRE=SSE3,SSSE3,SSE4_1,SSE4_2,AVX,AVX2"))
 434                  ("armhf-linux"
 435                   '("-DCPU_BASELINE_DISABLE=NEON")) ; causes build failures
 436                  ("aarch64-linux"
 437                   '("-DCPU_BASELINE=NEON"
 438                     "-DCPU_DISPATCH=NEON;VFPV3;FP16"))
 439                  (_ '()))
 440
 441              "-DBUILD_PERF_TESTS=OFF"
 442              "-DBUILD_TESTS=ON"
 443
 444              (string-append "-DOPENCV_EXTRA_MODULES_PATH=" (getcwd)
 445                             "/opencv-contrib/modules")
 446
 447              ;;Define test data:
 448              (string-append "-DOPENCV_TEST_DATA_PATH=" (getcwd)
 449                             "/opencv-extra/testdata")
 450
 451              ;; Is ON by default and would try to rebuild 3rd-party protobuf,
 452              ;; which we had removed, which would lead to an error:
 453              "-DBUILD_PROTOBUF=OFF"
 454
 455              ;; Rebuild protobuf files, because we have a slightly different
 456              ;; version than the included one. If we would not update, we
 457              ;; would get a compile error later:
 458              "-DPROTOBUF_UPDATE_FILES=ON"
 459
 460              ;; xfeatures2d disabled, because it downloads extra binaries from
 461              ;; https://github.com/opencv/opencv_3rdparty
 462              ;; defined in xfeatures2d/cmake/download_{vgg|bootdesc}.cmake
 463              ;; Cmp this bug entry:
 464              ;; https://github.com/opencv/opencv_contrib/issues/1131
 465              "-DBUILD_opencv_xfeatures2d=OFF")
 466        #:phases
 467        (modify-phases %standard-phases
 468          (add-after 'unpack 'disable-broken-tests
 469            (lambda _
 470              ;; These tests fails with:
 471              ;; vtkXOpenGLRenderWindow (0x723990): Could not find a decent config
 472              ;; I think we have no OpenGL support with the Xvfb.
 473              (substitute* '("modules/viz/test/test_tutorial3.cpp"
 474                             "modules/viz/test/test_main.cpp"
 475                             "modules/viz/test/tests_simple.cpp"
 476                             "modules/viz/test/test_viz3d.cpp")
 477                (("(TEST\\(Viz, )([a-z].*\\).*)" all pre post)
 478                 (string-append pre "DISABLED_" post)))
 479
 480              ;; This one fails with "unknown file: Failure"
 481              ;; But I couldn't figure out which file was missing:
 482              (substitute* "../opencv-contrib/modules/face/test/test_face_align.cpp"
 483                (("(TEST\\(CV_Face_FacemarkKazemi, )(can_detect_landmarks\\).*)"
 484                  all pre post)
 485                 (string-append pre "DISABLED_" post)))
 486
 487              ;; Failure reason: Bad accuracy
 488              ;; Incorrect count of accurate poses [2nd case]: 90.000000 / 94.000000
 489              (substitute* "../opencv-contrib/modules/rgbd/test/test_odometry.cpp"
 490                (("(TEST\\(RGBD_Odometry_Rgbd, )(algorithmic\\).*)" all pre post)
 491                 (string-append pre "DISABLED_" post)))
 492              #t))
 493
 494          (add-after 'unpack 'unpack-submodule-sources
 495            (lambda* (#:key inputs #:allow-other-keys)
 496              (mkdir "../opencv-extra")
 497              (mkdir "../opencv-contrib")
 498              (copy-recursively (assoc-ref inputs "opencv-extra")
 499                                "../opencv-extra")
 500              (invoke "tar" "xvf"
 501                      (assoc-ref inputs "opencv-contrib")
 502                      "--strip-components=1"
 503                      "-C" "../opencv-contrib")))
 504
 505          (add-after 'set-paths 'add-ilmbase-include-path
 506            (lambda* (#:key inputs #:allow-other-keys)
 507            ;; OpenEXR propagates ilmbase, but its include files do not appear
 508            ;; in the CPATH, so we need to add "$ilmbase/include/OpenEXR/" to
 509            ;; the CPATH to satisfy the dependency on "ImathVec.h".
 510            (setenv "CPATH"
 511                    (string-append (assoc-ref inputs "ilmbase")
 512                                   "/include/OpenEXR"
 513                                   ":" (or (getenv "CPATH") "")))
 514            #t))
 515        (add-before 'check 'start-xserver
 516          (lambda* (#:key inputs #:allow-other-keys)
 517            (let ((xorg-server (assoc-ref inputs "xorg-server"))
 518                  (disp ":1"))
 519              (setenv "HOME" (getcwd))
 520              (setenv "DISPLAY" disp)
 521              ;; There must be a running X server and make check doesn't start one.
 522              ;; Therefore we must do it.
 523              (zero? (system (format #f "~a/bin/Xvfb ~a &" xorg-server disp)))))))))
 524     (native-inputs
 525      `(("pkg-config" ,pkg-config)
 526        ("xorg-server" ,xorg-server-for-tests) ; For running the tests
 527        ("opencv-extra"
 528         ,(origin
 529            (method git-fetch)
 530            (uri (git-reference
 531                   (url "https://github.com/opencv/opencv_extra")
 532                   (commit version)))
 533            (file-name (git-file-name "opencv_extra" version))
 534            (sha256
 535             (base32 "08p5xnq8n1jw8svvz0fnirfg7q8dm3p4a5dl7527s5xj0f9qn7lp"))))
 536        ("opencv-contrib"
 537         ,(origin
 538            (method git-fetch)
 539            (uri (git-reference
 540                   (url "https://github.com/opencv/opencv_contrib")
 541                   (commit version)))
 542            (file-name (git-file-name "opencv_contrib" version))
 543            (patches (search-patches "opencv-rgbd-aarch64-test-fix.patch"))
 544            (sha256
 545             (base32 "1f334glf39nk42mpqq6j732h3ql2mpz89jd4mcl678s8n73nfjh2"))))))
 546     (inputs `(("libjpeg" ,libjpeg-turbo)
 547               ("libpng" ,libpng)
 548               ("jasper" ,jasper)
 549               ;; ffmpeg 4.0 causes core dumps in tests.
 550               ("ffmpeg" ,ffmpeg-3.4)
 551               ("libtiff" ,libtiff)
 552               ("hdf5" ,hdf5)
 553               ("libgphoto2" ,libgphoto2)
 554               ("libwebp" ,libwebp)
 555               ("zlib" ,zlib)
 556               ("gtkglext" ,gtkglext)
 557               ("openexr" ,openexr)
 558               ("ilmbase" ,ilmbase)
 559               ("gtk+" ,gtk+-2)
 560               ("python-numpy" ,python-numpy)
 561               ("protobuf" ,protobuf)
 562               ("vtk" ,vtk)
 563               ("python" ,python)))
 564     ;; These three CVEs are not a problem of OpenCV, see:
 565     ;; https://github.com/opencv/opencv/issues/10998
 566     (properties '((lint-hidden-cve . ("CVE-2018-7712"
 567                                       "CVE-2018-7713"
 568                                       "CVE-2018-7714"))))
 569     (synopsis "Computer vision library")
 570     (description "OpenCV is a library aimed at
 571 real-time computer vision, including several hundred computer
 572 vision algorithms.  It can be used to do things like:
 573
 574 @itemize
 575 @item image and video input and output
 576 @item image and video processing
 577 @item displaying
 578 @item feature recognition
 579 @item segmentation
 580 @item facial recognition
 581 @item stereo vision
 582 @item structure from motion
 583 @item augmented reality
 584 @item machine learning
 585 @end itemize\n")
 586     (home-page "https://opencv.org/")
 587     (license license:bsd-3)))
 588
 589 (define-public vips
 590   (package
 591     (name "vips")
 592     (version "8.10.6")
 593     (source
 594      (origin
 595        (method url-fetch)
 596        (uri (string-append
 597              "https://github.com/libvips/libvips/releases/download/v"
 598              version "/vips-" version ".tar.gz"))
 599        (sha256
 600         (base32 "0vjsh3i0861f6h9as3bch956cidz824zz499pvhjs3lfjn6hhs14"))))
 601     (build-system gnu-build-system)
 602     (native-inputs
 603      `(("gobject-introspection" ,gobject-introspection)
 604        ("pkg-config" ,pkg-config)))
 605     (inputs
 606      `(("expat" ,expat)
 607        ("fftw" ,fftw)
 608        ("giflib" ,giflib)
 609        ("glib" ,glib)
 610        ("hdf5" ,hdf5)
 611        ("imagemagick" ,imagemagick)
 612        ("lcms" ,lcms)
 613        ("libexif" ,libexif)
 614        ("libgsf" ,libgsf)
 615        ("libjpeg" ,libjpeg-turbo)
 616        ("libpng" ,libpng)
 617        ("librsvg" ,librsvg)
 618        ("libtiff" ,libtiff)
 619        ("libxml2" ,libxml2)
 620        ("libwebp" ,libwebp)
 621        ("matio" ,matio)
 622        ("niftilib" ,niftilib)
 623        ("openexr" ,openexr)
 624        ("orc" ,orc)
 625        ("pango" ,pango)
 626        ("poppler" ,poppler)))
 627     (home-page "https://libvips.github.io/libvips/")
 628     (synopsis "Multithreaded image processing system with low memory needs")
 629     (description
 630      "VIPS is a demand-driven, horizontally threaded image processing library.
 631 It's particularly good at processing large images, working with colour,
 632 scientific analysis, and general research & development.
 633
 634 Compared to most image processing libraries VIPS needs little RAM and runs
 635 quickly, especially on machines with more than one CPU core.  This is primarily
 636 due to its architecture which automatically parallelises the image workflows.")
 637     (license license:lgpl2.1+)))
 638
 639 (define-public gmic
 640   (package
 641     (name "gmic")
 642     (version "2.9.7")
 643     (source
 644      (origin
 645        (method url-fetch)
 646        (uri (string-append "https://gmic.eu/files/source/gmic_"
 647                            version ".tar.gz"))
 648        (sha256
 649         (base32 "05kzaplsl5qvxs7v6g73q0lq8dii8g6v77ap609188m7gr43f9cl"))))
 650     (build-system cmake-build-system)
 651     (arguments
 652      `(#:tests? #f ;there are no tests
 653        #:configure-flags '("-DBUILD_LIB_STATIC=OFF"
 654                            "-DENABLE_DYNAMIC_LINKING=ON"
 655                            "-DENABLE_LTO=ON")
 656        #:phases
 657        (modify-phases %standard-phases
 658          (add-before 'configure 'set-LDFLAGS
 659            (lambda* (#:key inputs outputs #:allow-other-keys)
 660              (setenv "LDFLAGS"
 661                      (string-append
 662                       "-Wl,-rpath="
 663                       (assoc-ref outputs "out") "/lib")))))))
 664     (native-inputs
 665      `(("pkg-config" ,pkg-config)))
 666     (inputs
 667      `(("curl" ,curl)
 668        ("fftw" ,fftw)
 669        ("graphicsmagick" ,graphicsmagick)
 670        ("libjpeg-turbo" ,libjpeg-turbo)
 671        ("libpng" ,libpng)
 672        ("libtiff" ,libtiff)
 673        ("libx11" ,libx11)
 674        ;;("opencv" ,opencv) ;OpenCV is currently broken in the CI
 675        ("openexr" ,openexr)
 676        ("zlib" ,zlib)))
 677     (home-page "https://gmic.eu/")
 678     (synopsis "Full-featured framework for digital image processing")
 679     (description "G'MIC is a full-featured framework for digital image
 680 processing.  It provides several user interfaces to convert / manipulate
 681 / filter / visualize generic image datasets, ranging from 1D scalar
 682 signals to 3D+t sequences of multi-spectral volumetric images, hence
 683 including 2D color images.")
 684     ;; Dual-licensed, either license applies.
 685     (license (list license:cecill license:cecill-c))))
 686
 687 (define-public gmic-qt
 688   (package
 689     (inherit gmic)
 690     (name "gmic-qt")
 691     (arguments
 692      (substitute-keyword-arguments (package-arguments gmic)
 693        ((#:configure-flags _)
 694         `(list "-DGMIC_QT_HOST=none" "-DENABLE_DYNAMIC_LINKING=ON"
 695                (string-append "-DGMIC_LIB_PATH="
 696                               (assoc-ref %build-inputs "gmic") "/lib")))
 697         ((#:phases phases)
 698          `(modify-phases ,phases
 699             (add-after 'unpack 'qt-chdir
 700               (lambda _ (chdir "gmic-qt") #t))))))
 701     (native-inputs
 702      `(("pkg-config" ,pkg-config)
 703        ("qttools" ,qttools)))
 704     (inputs
 705      `(("gmic" ,gmic)
 706        ("qtbase" ,qtbase)
 707        ,@(package-inputs gmic)))
 708     (synopsis "Qt frontend for the G'MIC image processing framework")
 709     (license license:gpl3+)))
 710
 711 (define-public gmic-qt-krita
 712   (package
 713     (inherit gmic-qt)
 714     (name "gmic-qt-krita")
 715     (arguments
 716      (substitute-keyword-arguments (package-arguments gmic-qt)
 717        ((#:configure-flags flags)
 718         '(list "-DGMIC_QT_HOST=krita" "-DENABLE_DYNAMIC_LINKING=ON"
 719                (string-append "-DGMIC_LIB_PATH="
 720                               (assoc-ref %build-inputs "gmic") "/lib")))))
 721     (synopsis "Krita plugin for the G'MIC image processing framework")))
 722
 723 (define-public nip2
 724   (package
 725     (name "nip2")
 726     (version "8.7.1")
 727     (source
 728      (origin
 729        (method url-fetch)
 730        (uri (string-append "https://github.com/libvips/nip2/releases/download/v"
 731                            version "/nip2-" version ".tar.gz" ))
 732        (sha256
 733         (base32 "0l7n427njif53npqn02gfjjly8y3khbrkzqxp10j5vp9h97psgiw"))))
 734     (build-system gnu-build-system)
 735     (arguments
 736      `(#:phases
 737        (modify-phases %standard-phases
 738          ;; test_conv.ws keep failing so disabling for now.
 739          (add-after 'unpack 'disable-test-conv
 740            (lambda _
 741              (delete-file "test/workspaces/test_conv.ws")
 742              #t))
 743          (add-before 'check 'set-home
 744            (lambda _
 745              (setenv "HOME" "/tmp") #t)))))
 746     (inputs
 747      `(("vips" ,vips)
 748        ("glib" ,glib)
 749        ("libtiff" ,libtiff)
 750        ("gtk+-2" ,gtk+-2)
 751        ("libxml2" ,libxml2)
 752        ("libexif" ,libexif)
 753        ("libjpeg" ,libjpeg-turbo)        ;required by vips.pc
 754        ("librsvg" ,librsvg)
 755        ("fftw" ,fftw)
 756        ("libgsf" ,libgsf)
 757        ("imagemagick" ,imagemagick)
 758        ("orc" ,orc)
 759        ("matio" ,matio)
 760        ("lcms" ,lcms)
 761        ("libwebp" ,libwebp)
 762        ("openexr" ,openexr)
 763        ("poppler" ,poppler)
 764        ("gsl" ,gsl)))
 765     (native-inputs
 766      `(("flex" ,flex)
 767        ("bison" ,bison)
 768        ("pkg-config" ,pkg-config)))
 769     (home-page "https://github.com/libvips/nip2")
 770     (synopsis "Spreadsheet-like GUI for libvips")
 771     (description "This package provide a graphical user interface (GUI) for
 772 the VIPS image processing library.  It's a little like a spreadsheet: you
 773 create a set of formula connecting your objects together, and on a change nip2
 774 recalculates.")
 775     (license license:gpl2+)))
 776
 777 (define-public vxl
 778   (package
 779     (name "vxl")
 780     (version "2.0.2")
 781     (source
 782      (origin
 783        (method git-fetch)
 784        (uri (git-reference
 785              (url "https://github.com/vxl/vxl")
 786              (commit (string-append "v" version))))
 787        (file-name (git-file-name name version))
 788        (sha256
 789         (base32 "0949hw57szq8943f1whwqaz591xjmb19kj803hcv74hdai2b0ycg"))
 790        (modules '((guix build utils)))
 791        ;; TODO: vxl includes an old version of dcmtk.  It won't build with
 792        ;; version 3.6.x.
 793        (snippet
 794         '(begin
 795            (for-each delete-file-recursively
 796                      '("v3p/bzlib/"
 797                        "v3p/geotiff/"
 798                        "v3p/jpeg/"
 799                        "v3p/png/"
 800                        "v3p/tiff/"
 801                        "v3p/zlib/"))
 802            (substitute* "v3p/CMakeLists.txt"
 803              (("add_subdirectory\\((tiff|png|jpeg|zlib|bzlib|geotiff)\\)")
 804               ""))
 805            #t))))
 806     (build-system cmake-build-system)
 807     (inputs
 808      `(("libgeotiff" ,libgeotiff)
 809        ("libtiff" ,libtiff)
 810        ("libjpeg" ,libjpeg-turbo)
 811        ("libpng" ,libpng)
 812        ("zlib" ,zlib)))
 813     (home-page "https://github.com/vxl/vxl/")
 814     (synopsis "Collection of C++ libraries for computer vision")
 815     (description "VXL (the Vision-something-Libraries) is a collection of C++
 816 libraries designed for computer vision research and implementation.")
 817     (license license:bsd-3)))
 818
 819 (define-public vxl-1
 820   (package (inherit vxl)
 821     (name "vxl")
 822     (version "1.18.0")
 823     (source
 824      (origin
 825        (method git-fetch)
 826        (uri (git-reference
 827              (url "https://github.com/vxl/vxl")
 828              (commit (string-append "v" version))))
 829        (file-name (git-file-name name version))
 830        (sha256
 831         (base32 "1g4mr2cc58jwm0vasscbd4y5380wj3ahkvq121z4gs83fhavvxgz"))
 832        (modules '((guix build utils)))
 833        (snippet
 834         '(begin
 835            (for-each delete-file-recursively
 836                      '("v3p/bzlib/"
 837                        "v3p/geotiff/"
 838                        "v3p/png/"
 839                        "v3p/tiff/"
 840                        "v3p/zlib/"))
 841            (substitute* "v3p/CMakeLists.txt"
 842              (("add_subdirectory\\((tiff|png|jpeg|zlib|bzlib|geotiff)\\)")
 843               ""))
 844            #t))))
 845     (arguments
 846      `(#:configure-flags
 847        ;; Needed for itk-snap
 848        (list "-DVNL_CONFIG_LEGACY_METHODS=ON")))))
 849
 850 (define-public insight-toolkit
 851   (package
 852     (name "insight-toolkit")
 853     (version "5.0.0")
 854     (source
 855      (origin
 856        (method url-fetch)
 857        (uri (string-append "https://github.com/InsightSoftwareConsortium/ITK/"
 858                            "releases/download/v" version "/InsightToolkit-"
 859                            version ".tar.xz"))
 860        (sha256
 861         (base32 "0bs63mk4q8jmx38f031jy5w5n9yy5ng9x8ijwinvjyvas8cichqi"))))
 862     (build-system cmake-build-system)
 863     (arguments
 864      `(#:tests? #f            ; tests require network access and external data
 865        #:configure-flags
 866        '("-DITK_USE_GPU=ON"
 867          "-DITK_USE_SYSTEM_LIBRARIES=ON"
 868          "-DITK_USE_SYSTEM_GOOGLETEST=ON"
 869          "-DITK_BUILD_SHARED=ON"
 870          ;; This prevents "GTest::GTest" from being added to the ITK_LIBRARIES
 871          ;; variable in the installed CMake files.  This is necessary as other
 872          ;; packages using insight-toolkit could not be configured otherwise.
 873          "-DGTEST_ROOT=gtest")
 874        #:phases
 875        (modify-phases %standard-phases
 876          (add-after 'unpack 'do-not-tune
 877            (lambda _
 878              (substitute* "CMake/ITKSetStandardCompilerFlags.cmake"
 879                (("-mute=native") ""))
 880              #t)))))
 881     (inputs
 882      `(("eigen" ,eigen)
 883        ("expat" ,expat)
 884        ("fftw" ,fftw)
 885        ("fftwf" ,fftwf)
 886        ("hdf5" ,hdf5)
 887        ("libjpeg" ,libjpeg-turbo)
 888        ("libpng" ,libpng)
 889        ("libtiff" ,libtiff)
 890        ("mesa" ,mesa-opencl)
 891        ("perl" ,perl)
 892        ("python" ,python)
 893        ("tbb" ,tbb)
 894        ("vxl" ,vxl-1)
 895        ("zlib" ,zlib)))
 896     (native-inputs
 897      `(("googletest" ,googletest)
 898        ("pkg-config" ,pkg-config)))
 899     (home-page "https://github.com/InsightSoftwareConsortium/ITK/")
 900     (synopsis "Scientific image processing, segmentation and registration")
 901     (description "The Insight Toolkit (ITK) is a toolkit for N-dimensional
 902 scientific image processing, segmentation, and registration.  Segmentation is
 903 the process of identifying and classifying data found in a digitally sampled
 904 representation.  Typically the sampled representation is an image acquired
 905 from such medical instrumentation as CT or MRI scanners.  Registration is the
 906 task of aligning or developing correspondences between data.  For example, in
 907 the medical environment, a CT scan may be aligned with a MRI scan in order to
 908 combine the information contained in both.")
 909     (license license:asl2.0)))
 910
 911 (define-public insight-toolkit-4
 912   (package (inherit insight-toolkit)
 913     (version "4.13.2")
 914     (source
 915      (origin
 916        (method url-fetch)
 917        (uri (string-append "https://github.com/InsightSoftwareConsortium/ITK/"
 918                            "releases/download/v" version "/InsightToolkit-"
 919                            version ".tar.xz"))
 920        (sha256
 921         (base32 "19cgfpd63gqrvc3m27m394gy2d7w79g5y6lvznb5qqr49lihbgns"))))
 922     (arguments
 923      `(#:tests? #f            ; tests require network access and external data
 924        #:configure-flags
 925        '("-DITKV3_COMPATIBILITY=ON"     ; needed for itk-snap
 926          "-DITK_USE_GPU=ON"
 927          "-DITK_USE_SYSTEM_LIBRARIES=ON"
 928          "-DITK_USE_SYSTEM_GOOGLETEST=ON"
 929          "-DITK_USE_SYSTEM_VXL=ON")))))
 930
 931 (define-public insight-toolkit-4.12
 932   (package (inherit insight-toolkit-4)
 933     (version "4.12.2")
 934     (source
 935      (origin
 936        (method url-fetch)
 937        (uri (string-append "mirror://sourceforge/itk/itk/4.12/"
 938                            "InsightToolkit-" version ".tar.xz"))
 939        (sha256
 940         (base32 "1qw9mxbh083siljygahl4gdfv91xvfd8hfl7ghwii19f60xrvn2w"))))))
 941
 942 (define-public itk-snap
 943   (package
 944     (name "itk-snap")
 945     (version "3.8.0")
 946     (source
 947      (origin
 948        (method git-fetch)
 949        (uri (git-reference
 950              (url "https://git.code.sf.net/p/itk-snap/src")
 951              (commit (string-append "v" version))))
 952        (file-name (git-file-name name version))
 953        (sha256
 954         (base32 "15i5ixpryfrbf3vrrb5rici8fb585f25k0v1ljds16bp1f1msr4q"))))
 955     (build-system cmake-build-system)
 956     (arguments
 957      `(#:configure-flags
 958        (list "-DSNAP_VERSION_GIT_SHA1=release"
 959              "-DSNAP_VERSION_GIT_BRANCH=release"
 960              "-DSNAP_VERSION_GIT_TIMESTAMP=0"
 961              "-DSNAP_PACKAGE_QT_PLUGINS=OFF"
 962              "-DCMAKE_POSITION_INDEPENDENT_CODE=ON")
 963        #:phases
 964        (modify-phases %standard-phases
 965          ;; During the installation phase all libraries provided by all
 966          ;; dependencies will be copied to the lib directory.  That's insane,
 967          ;; so we disable this.
 968          (add-after 'unpack 'do-not-copy-dependencies
 969            (lambda _
 970              (substitute* "CMakeLists.txt"
 971                (("install_qt5_executable\
 972 \\(\\$\\{SNAP_MAIN_INSTALL_DIR\\}/\\$\\{SNAP_EXE\\}\\)")
 973                 ""))
 974              #t))
 975          (add-after 'unpack 'disable-gui-tests
 976            (lambda _
 977              ;; The GUI tests just time out.
 978              (substitute* "CMakeLists.txt"
 979                (("  (Workspace|DiffSpace|ProbeIntensity|RegionCompetition\
 980 |RandomForest|RandomForestBailOut)")
 981                 ""))
 982              #t))
 983          (add-after 'unpack 'make-reproducible
 984            (lambda _
 985              (substitute* "CMakeLists.txt"
 986                (("TODAY\\(SNAP_VERSION_COMPILE_DATE\\)")
 987                 "SET(SNAP_VERSION_COMPILE_DATE \"(removed for reproducibility)\")"))
 988              #t))
 989          (add-after 'unpack 'prepare-submodules
 990            (lambda* (#:key inputs #:allow-other-keys)
 991              (rmdir "Submodules/c3d")
 992              (copy-recursively (assoc-ref inputs "c3d-src")
 993                                "Submodules/c3d")
 994              (substitute* '("Submodules/c3d/adapters/BiasFieldCorrectionN4.cxx"
 995                             "Submodules/c3d/adapters/ApplyMetric.cxx")
 996                (("vcl_") "std::"))
 997              (rmdir "Submodules/greedy")
 998              (symlink (assoc-ref inputs "greedy-src")
 999                       "Submodules/greedy")
1000              #t))
1001          (add-after 'unpack 'fix-includes
1002            (lambda _
1003              (substitute* "GUI/Model/RegistrationModel.cxx"
1004                (("<vnl_symmetric_eigensystem.h>")
1005                 "<vnl/algo/vnl_symmetric_eigensystem.h>"))
1006              #t))
1007          (add-before 'check 'prepare-tests
1008            (lambda _
1009              ;; Needed by at least one test.
1010              (setenv "HOME" "/tmp")
1011              #t))
1012          (add-after 'install 'wrap-executable
1013            (lambda* (#:key inputs outputs #:allow-other-keys)
1014              (let ((out (assoc-ref outputs "out")))
1015                (wrap-program (string-append out "/bin/itksnap")
1016                  `("QT_PLUGIN_PATH" ":" prefix
1017                    ,(map (lambda (label)
1018                            (string-append (assoc-ref inputs label)
1019                                           "/lib/qt5/plugins"))
1020                          '("qtbase" "qtdeclarative"))))
1021                #t))))))
1022     (inputs
1023      `(("curl" ,curl)
1024        ("fftw" ,fftw)
1025        ("fftwf" ,fftwf)
1026        ("glu" ,glu)
1027        ("hdf5" ,hdf5)
1028        ("mesa" ,mesa-opencl)
1029        ;; This package does not build with either insight-toolkit 5.0.0 and
1030        ;; not with 4.13.  It really needs to be 4.12.
1031        ("itk" ,insight-toolkit-4.12)
1032        ("vtk" ,vtk-6)
1033        ("qtbase" ,qtbase)
1034        ("qtdeclarative" ,qtdeclarative)
1035        ("vxl" ,vxl-1)
1036        ("zlib" ,zlib)))
1037     (native-inputs
1038      `(("googletest" ,googletest)
1039        ("qttools" ,qttools)
1040        ("pkg-config" ,pkg-config)
1041        ("c3d-src"
1042         ,(let* ((commit "f521358db26e00002c911cc47bf463b043942ad3")
1043                 (revision "1")
1044                 (version (git-version "0" revision commit)))
1045            (origin
1046              (method git-fetch)
1047              (uri (git-reference
1048                    (url "https://github.com/pyushkevich/c3d")
1049                    (commit commit)))
1050              (file-name (git-file-name "c3d" version))
1051              (sha256
1052               (base32
1053                "0kyv3rxrxwr8c3sa9zv01lsnhk95b27gx1s870k3yi8qp52h7bx3")))))
1054        ;; We are using an arbitrary commit from 2017 because the latest
1055        ;; version breaks the build...
1056        ("greedy-src"
1057         ,(let* ((commit "97e340f7e8e66597599144947775e6039e79a0d3")
1058                 (revision "1")
1059                 (version (git-version "0" revision commit)))
1060            (origin
1061              (method git-fetch)
1062              (uri (git-reference
1063                    (url "https://github.com/pyushkevich/greedy")
1064                    (commit commit)))
1065              (file-name (git-file-name "greedy" version))
1066              (sha256
1067               (base32
1068                "0k5bc9za4jrc8z9dj08z1rkcp5xf0gnd1d2jmi1w9ny4vxh2q2ab")))))))
1069     (home-page "https://sourceforge.net/p/itk-snap/")
1070     (synopsis "Medical image segmentation")
1071     (description "ITK-SNAP is a tool for segmenting anatomical structures in
1072 medical images.  It provides an automatic active contour segmentation
1073 pipeline, along with supporting a manual segmentation toolbox.  ITK-SNAP has a
1074 full-featured UI aimed at clinical researchers.")
1075     ;; This includes the submodules greedy and c3d.
1076     (license license:gpl3+)))
1077
1078 (define-public metapixel
1079   ;; Follow stable branch.
1080   (let ((commit "98ee9daa093b6c334941242e63f90b1c2876eb4f"))
1081     (package
1082       (name "metapixel")
1083       (version (git-version "1.0.2" "1" commit))
1084       (source
1085        (origin
1086          (method git-fetch)
1087          (uri (git-reference
1088                (url "https://github.com/schani/metapixel")
1089                (commit commit)
1090                ;; TODO: Package rwimg and lispreader?
1091                (recursive? #t)))
1092          (file-name (git-file-name name version))
1093          (sha256
1094           (base32 "0r7n3a6bvcxkbpda4mwmrpicii09iql5z69nkjqygkwxw7ny3309"))))
1095       (build-system gnu-build-system)
1096       (inputs
1097        `(("giflib" ,giflib)
1098          ("libjpeg" ,libjpeg-turbo)
1099          ("libpng" ,libpng)
1100          ("perl" ,perl)))
1101       (native-inputs
1102        `(("pkg-config" ,pkg-config)
1103          ("docbook-xml" ,docbook-xml)
1104          ("docbook-xsl" ,docbook-xsl)
1105          ("xsltproc" ,libxslt)))
1106       (arguments
1107        `(#:tests? #f                    ; No tests.
1108          #:make-flags (list
1109                        (string-append "PREFIX=" (assoc-ref %outputs "out"))
1110                        (string-append "MANPAGE_XSL="
1111                                       (assoc-ref %build-inputs "docbook-xsl")
1112                                       "/xml/xsl/docbook-xsl-*/manpages/docbook.xsl"))
1113          #:phases
1114          (modify-phases %standard-phases
1115            (delete 'configure)
1116            (add-before 'install 'make-local-docbook-xml
1117              (lambda* (#:key inputs #:allow-other-keys)
1118                (substitute* "metapixel.xml"
1119                  (("http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd")
1120                   (string-append (assoc-ref inputs "docbook-xml")
1121                                  "/xml/dtd/docbook/docbookx.dtd")))
1122                #t))
1123            (add-before 'install 'fix-directory-creation
1124              (lambda* (#:key outputs #:allow-other-keys)
1125                (mkdir-p (string-append (assoc-ref outputs "out") "/share/man/man1"))
1126                #t)))))
1127       (home-page "https://www.complang.tuwien.ac.at/schani/metapixel/")
1128       (synopsis "Photomosaics generator")
1129       (description "Metapixel is a program for generating photomosaics.  It can
1130 generate classical photomosaics, in which the source image is viewed as a
1131 matrix of equally sized rectangles for each of which a matching image is
1132 substituted, as well as collage-style photomosaics, in which rectangular parts
1133 of the source image at arbitrary positions (i.e. not aligned to a matrix) are
1134 substituted by matching images.")
1135       (license license:gpl2))))
1136
1137 (define-public scantailor-advanced
1138   (let ((commit "3d1e74e6ace413733511086934a66f4e3f7a6027"))
1139     (package
1140       (name "scantailor-advanced")
1141       (version (string-append "1.0.16-" (string-take commit 7)))
1142       (source
1143        (origin
1144          (method git-fetch)
1145          (uri (git-reference
1146                (url "https://github.com/4lex4/scantailor-advanced")
1147                (commit commit)))
1148          (file-name (git-file-name name version))
1149          (sha256
1150           (base32
1151            "0kixwjb2x457dq7927hkh34c803p7yh1pmn6n61rk9shqrcg492h"))))
1152       (build-system qt-build-system)
1153       (native-inputs
1154        `(("qttools" ,qttools)))
1155       (inputs
1156        `(("boost" ,boost)
1157          ("libjpeg" ,libjpeg-turbo)
1158          ("libpng" ,libpng)
1159          ("libtiff" ,libtiff)
1160          ("qtbase" ,qtbase)
1161          ("qtsvg" ,qtsvg)
1162          ("zlib" ,zlib)))
1163       (arguments
1164        `(#:phases
1165          (modify-phases %standard-phases
1166            ;; Some tests require a display and fail with offscreen mode.
1167            (add-after 'unpack 'disable-failing-tests
1168              (lambda _
1169                (setenv "ARGS" "--exclude-regex \"imageproc_.*\"")
1170                #t)))))
1171       (home-page "https://github.com/4lex4/scantailor-advanced")
1172       (synopsis "Clean up scanned pages")
1173       (description "Scan Tailor is an interactive post-processing tool for
1174 scanned pages.  It performs operations such as page splitting, deskewing,
1175 adding/removing borders, and others.  You give it raw scans, and you get pages
1176 ready to be printed or assembled into a PDF or DJVU file.  Scanning, optical
1177 character recognition, and assembling multi-page documents are out of scope of
1178 this project.
1179
1180 Scan Tailer Advanced is a fork of Scan Tailer that merges Scan Tailor Featured
1181 and Scan Tailor Enhanced versions as well as including many more bug fixes.")
1182       (license license:gpl3+))))
1183
1184 (define-public stiff
1185   (package
1186     (name "stiff")
1187     (version "2.4.0")
1188     (source
1189      (origin
1190        (method url-fetch)
1191        (uri (string-append "https://www.astromatic.net/download/stiff/stiff-"
1192                            version ".tar.gz"))
1193        (sha256
1194         (base32 "14m92dskzw7bwsr64ha4p0mj3ndv13gwcbfic3qxrs3zq5353s7l"))))
1195     (build-system gnu-build-system)
1196     (inputs
1197      `(("libtiff" ,libtiff)
1198        ("zlib" ,zlib)
1199        ("libjpeg-turbo" ,libjpeg-turbo)))
1200     (home-page "https://www.astromatic.net/software/stiff")
1201     (synopsis "Convert scientific FITS images to TIFF format")
1202     (description
1203      "STIFF is a program that converts scientific @acronym{FITS, Flexible Image
1204 Transport System} images to the more popular TIFF format for illustration
1205 purposes.")
1206     (license license:gpl3+)))