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 ;;; Copyright © 2021 Paul Garlick <pgarlick@tourbillion-technology.com>
  20 ;;; Copyright © 2021 Guillaume Le Vaillant <glv@posteo.net>
  21 ;;; Copyright © 2021 Ivan Gankevich <i.gankevich@spbu.ru>
  22 ;;;
  23 ;;; This file is part of GNU Guix.
  24 ;;;
  25 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  26 ;;; under the terms of the GNU General Public License as published by
  27 ;;; the Free Software Foundation; either version 3 of the License, or (at
  28 ;;; your option) any later version.
  29 ;;;
  30 ;;; GNU Guix is distributed in the hope that it will be useful, but
  31 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  32 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  33 ;;; GNU General Public License for more details.
  34 ;;;
  35 ;;; You should have received a copy of the GNU General Public License
  36 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  37
  38 (define-module (gnu packages image-processing)
  39   #:use-module ((guix licenses) #:prefix license:)
  40   #:use-module (guix packages)
  41   #:use-module (guix utils)
  42   #:use-module (guix download)
  43   #:use-module (guix git-download)
  44   #:use-module (guix build-system qt)
  45   #:use-module (guix build-system cmake)
  46   #:use-module (guix build-system gnu)
  47   #:use-module (guix build-system python)
  48   #:use-module (gnu packages)
  49   #:use-module (gnu packages algebra)
  50   #:use-module (gnu packages bison)
  51   #:use-module (gnu packages boost)
  52   #:use-module (gnu packages check)
  53   #:use-module (gnu packages compression)
  54   #:use-module (gnu packages curl)
  55   #:use-module (gnu packages docbook)
  56   #:use-module (gnu packages documentation)
  57   #:use-module (gnu packages flex)
  58   #:use-module (gnu packages fontutils)
  59   #:use-module (gnu packages geo)
  60   #:use-module (gnu packages ghostscript)
  61   #:use-module (gnu packages gimp)
  62   #:use-module (gnu packages gl)
  63   #:use-module (gnu packages glib)
  64   #:use-module (gnu packages gnome)
  65   #:use-module (gnu packages graphics)
  66   #:use-module (gnu packages graphviz)
  67   #:use-module (gnu packages gstreamer)
  68   #:use-module (gnu packages gtk)
  69   #:use-module (gnu packages icu4c)
  70   #:use-module (gnu packages image)
  71   #:use-module (gnu packages imagemagick)
  72   #:use-module (gnu packages maths)
  73   #:use-module (gnu packages pdf)
  74   #:use-module (gnu packages perl)
  75   #:use-module (gnu packages photo)
  76   #:use-module (gnu packages pkg-config)
  77   #:use-module (gnu packages protobuf)
  78   #:use-module (gnu packages python)
  79   #:use-module (gnu packages python-check)
  80   #:use-module (gnu packages python-xyz)
  81   #:use-module (gnu packages qt)
  82   #:use-module (gnu packages serialization)
  83   #:use-module (gnu packages sqlite)
  84   #:use-module (gnu packages tbb)
  85   #:use-module (gnu packages tls)
  86   #:use-module (gnu packages version-control)
  87   #:use-module (gnu packages video)
  88   #:use-module (gnu packages xiph)
  89   #:use-module (gnu packages xml)
  90   #:use-module (gnu packages xorg)
  91   #:use-module (ice-9 match)
  92   #:use-module (srfi srfi-1))
  93
  94 (define-public dcmtk
  95   (package
  96     (name "dcmtk")
  97     (version "3.6.6")
  98     (source
  99      (origin
 100        (method url-fetch)
 101        (uri
 102         (string-append "ftp://dicom.offis.de/pub/dicom/offis/software/dcmtk/"
 103                        "dcmtk" (string-join (string-split version #\.) "")
 104                        "/dcmtk-" version ".tar.gz"))
 105        (sha256
 106         (base32 "13j5yf3p6qj3mr17d77r3kcqchf055hgvk1w15vmdr8f54mwcnb8"))))
 107     (build-system cmake-build-system)
 108     (inputs
 109      (list icu4c
 110            libjpeg-turbo
 111            libpng
 112            libtiff
 113            libxml2
 114            openssl
 115            zlib))
 116     (native-inputs
 117      (list doxygen))           ; for HTML documentation
 118     (home-page "https://dcmtk.org")
 119     (synopsis "Libraries and programs implementing parts of the DICOM standard")
 120     (description "DCMTK is a collection of libraries and applications
 121 implementing large parts the DICOM standard.  It includes software for
 122 examining, constructing and converting DICOM image files, handling offline
 123 media, sending and receiving images over a network connection, as well as
 124 demonstrative image storage and worklist servers.")
 125     (license (license:fsf-free
 126               "file://COPYRIGHT"
 127               "A union of the Apache 2.0 licence and various non-copyleft
 128 licences similar to the Modified BSD licence."))))
 129
 130 (define-public mia
 131   (package
 132     (name "mia")
 133     (version "2.4.6")
 134     (source (origin
 135               (method url-fetch)
 136               (uri (string-append "mirror://sourceforge/mia/mia/"
 137                                   (version-major+minor version)
 138                                   "/mia-" version ".tar.xz"))
 139               (sha256
 140                (base32
 141                 "0j4nd5z7i3v199jh7hqqhwd4g7snchizkc7rhzanpvngqg91m1pb"))))
 142     (build-system cmake-build-system)
 143     (arguments
 144      `(#:configure-flags
 145        (list "-DMIA_CREATE_NIPYPE_INTERFACES=0"
 146              "-DCMAKE_CXX_FLAGS=-fpermissive")))
 147     (inputs
 148      `(("boost" ,boost)
 149        ("dcmtk" ,dcmtk)
 150        ("doxygen" ,doxygen)
 151        ("eigen" ,eigen)
 152        ("fftw" ,fftw)
 153        ("fftwf" ,fftwf)
 154        ("gsl" ,gsl)
 155        ("gts" ,gts)
 156        ("hdf5" ,hdf5)
 157        ("itpp" ,itpp)
 158        ("libjpeg" ,libjpeg-turbo)
 159        ("libpng" ,libpng)
 160        ("libtiff" ,libtiff)
 161        ("libxml" ,libxml2)
 162        ("libxml++" ,libxml++)
 163        ("maxflow" ,maxflow)
 164        ("niftilib" ,niftilib)
 165        ("nlopt" ,nlopt)
 166        ("openexr" ,openexr-2)
 167        ("python-lxml" ,python2-lxml)
 168        ("vtk" ,vtk)))
 169     (native-inputs
 170      `(("pkg-config" ,pkg-config)
 171        ("python" ,python-2)))
 172     (home-page "http://mia.sourceforge.net")
 173     (synopsis "Toolkit for gray scale medical image analysis")
 174     (description "MIA provides a combination of command line tools, plug-ins,
 175 and libraries that make it possible run image processing tasks interactively
 176 in a command shell and to prototype using the shell's scripting language.  It
 177 is built around a plug-in structure that makes it easy to add functionality
 178 without compromising the original code base and it makes use of a wide variety
 179 of external libraries that provide additional functionality.")
 180     (license license:gpl3+)))
 181
 182 (define-public opencolorio
 183   (package
 184     (name "opencolorio")
 185     (version "1.1.1")
 186     (source
 187      (origin
 188        (method git-fetch)
 189        (uri (git-reference
 190              (url "https://github.com/AcademySoftwareFoundation/OpenColorIO")
 191              (commit (string-append "v" version))))
 192        (sha256
 193         (base32 "12srvxca51czpfjl0gabpidj9n84mw78ivxy5w75qhq2mmc798sb"))
 194        (file-name (git-file-name name version))
 195        (modules '((guix build utils)))
 196        (snippet
 197         `(begin
 198            ;; Remove bundled tarballs, patches, and .jars(!).  XXX: Upstream
 199            ;; claims to have fixed USE_EXTERNAL_YAML, but it still fails with:
 200            ;; https://github.com/AcademySoftwareFoundation/OpenColorIO/issues/517
 201            ;; When removing it, also remove it from the licence field comment.
 202            (for-each delete-file-recursively
 203                      (filter
 204                       (lambda (full-name)
 205                         (let ((file (basename full-name)))
 206                           (not (or (string-prefix? "yaml-cpp-0.3" file)
 207                                    (string=? "unittest.h" file)))))
 208                       (find-files "ext" ".*")))
 209
 210            #t))))
 211     (build-system cmake-build-system)
 212     (arguments
 213      `(#:configure-flags
 214        (list (string-append "-DCMAKE_CXX_FLAGS="
 215                             "-Wno-error=deprecated-declarations "
 216                             "-Wno-error=unused-function")
 217              "-DOCIO_BUILD_STATIC=OFF"
 218              ;; "-DUSE_EXTERNAL_YAML=ON"
 219              "-DUSE_EXTERNAL_TINYXML=ON"
 220              "-DUSE_EXTERNAL_LCMS=ON")
 221        #:phases
 222        (modify-phases %standard-phases
 223          (add-after 'unpack 'patch-test-suite
 224            (lambda _
 225              (substitute* "src/core_tests/CMakeLists.txt"
 226                (("/bin/sh") (which "bash")))
 227              #t)))))
 228     (native-inputs
 229      (list git pkg-config))
 230     (inputs
 231      ;; XXX Adding freeglut, glew, ilmbase, mesa, and openimageio for
 232      ;; ocioconvert fails: error: conflicting declaration ?typedef void
 233      ;; (* PFNGLGETFRAGMENTMATERIALFVSGIXPROC)(GLenum, GLenum, GLfloat*)
 234      (list lcms openexr-2 tinyxml))
 235     (home-page "https://opencolorio.org")
 236     (synopsis "Color management for visual effects and animation")
 237     (description
 238      "OpenColorIO, or OCIO, is a complete color management solution geared
 239 towards motion picture production, with an emphasis on visual effects and
 240 computer animation.  It provides a straightforward and consistent user
 241 experience across all supporting applications while allowing for sophisticated
 242 back-end configuration options suitable for high-end production usage.
 243
 244 OCIO is compatible with the @acronym{ACES, Academy Color Encoding
 245 Specification} and is @acronym{LUT, look-up table}-format agnostic, supporting
 246 many popular formats.")
 247     (license (list license:expat        ; docs/ociotheme/static, ext/yaml-cpp-*
 248                    license:zlib         ; src/core/md5
 249                    license:bsd-3))))    ; the rest
 250
 251 (define-public vtk
 252   (package
 253     (name "vtk")
 254     (version "9.0.1")
 255     (source (origin
 256               (method url-fetch)
 257               (uri (string-append "https://vtk.org/files/release/"
 258                                   (version-major+minor version)
 259                                   "/VTK-" version ".tar.gz"))
 260               (sha256
 261                (base32
 262                 "1ir2lq9i45ls374lcmjzw0nrm5l5hnm1w47lg8g8d0n2j7hsaf8v"))
 263               (patches
 264                (search-patches "vtk-fix-freetypetools-build-failure.patch"))
 265               (modules '((guix build utils)))
 266               (snippet
 267                '(begin
 268                   (for-each
 269                     (lambda (dir)
 270                       (delete-file-recursively
 271                         (string-append "ThirdParty/" dir "/vtk" dir)))
 272                     ;; pugixml depended upon unconditionally
 273                     '("doubleconversion" "eigen" "expat" "freetype" "gl2ps"
 274                       "glew" "hdf5" "jpeg" "jsoncpp" "libproj" "libxml2" "lz4"
 275                       "netcdf" "ogg" "png" "sqlite" "theora" "tiff" "zlib"))
 276                   #t))))
 277     (properties `((release-monitoring-url . "https://vtk.org/download/")))
 278     (build-system cmake-build-system)
 279     (arguments
 280      '(#:build-type "Release"           ;Build without '-g' to save space.
 281        #:configure-flags '(;"-DBUILD_TESTING:BOOL=TRUE"
 282                            ;    ; not honored
 283                            "-DVTK_USE_EXTERNAL=OFF" ;; default
 284                            "-DVTK_MODULE_USE_EXTERNAL_VTK_doubleconversion=ON"
 285                            "-DVTK_MODULE_USE_EXTERNAL_VTK_eigen=ON"
 286                            "-DVTK_MODULE_USE_EXTERNAL_VTK_expat=ON"
 287                            "-DVTK_MODULE_USE_EXTERNAL_VTK_freetype=ON"
 288                            "-DVTK_MODULE_USE_EXTERNAL_VTK_gl2ps=ON"
 289                            "-DVTK_MODULE_USE_EXTERNAL_VTK_glew=ON"
 290                            "-DVTK_MODULE_USE_EXTERNAL_VTK_hdf5=ON"
 291                            "-DVTK_MODULE_USE_EXTERNAL_VTK_jpeg=ON"
 292                            "-DVTK_MODULE_USE_EXTERNAL_VTK_jsoncpp=ON"
 293                            "-DVTK_MODULE_USE_EXTERNAL_VTK_libproj=ON"
 294                            "-DVTK_MODULE_USE_EXTERNAL_VTK_libxml2=ON"
 295                            "-DVTK_MODULE_USE_EXTERNAL_VTK_lz4=ON"
 296                            "-DVTK_MODULE_USE_EXTERNAL_VTK_netcdf=ON"
 297                            "-DVTK_MODULE_USE_EXTERNAL_VTK_ogg=ON"
 298                            "-DVTK_MODULE_USE_EXTERNAL_VTK_png=ON"
 299                            ;"-DVTK_MODULE_USE_EXTERNAL_VTK_pugixml=ON"    ; breaks IO/CityGML
 300                            "-DVTK_MODULE_USE_EXTERNAL_VTK_sqlite=ON"
 301                            "-DVTK_MODULE_USE_EXTERNAL_VTK_theora=ON"
 302                            "-DVTK_MODULE_USE_EXTERNAL_VTK_tiff=ON"
 303                            "-DVTK_MODULE_USE_EXTERNAL_VTK_zlib=ON"
 304                            "-DVTK_WRAP_PYTHON=ON"
 305                            "-DVTK_PYTHON_VERSION:STRING=3"
 306                            )
 307        #:phases
 308          (modify-phases %standard-phases
 309            (add-after 'unpack 'patch-sources
 310              (lambda _
 311                (substitute* "Common/Core/vtkFloatingPointExceptions.cxx"
 312                  (("<fenv.h>") "<cfenv>"))
 313                (substitute* "Common/Core/CMakeLists.txt"
 314                  (("fenv.h") "cfenv")))))
 315        #:tests? #f))        ;XXX: test data not included
 316     (inputs
 317      `(("double-conversion" ,double-conversion)
 318        ("eigen" ,eigen)
 319        ("expat" ,expat)
 320        ("freetype" ,freetype)
 321        ("gl2ps" ,gl2ps)
 322        ("glew" ,glew)
 323        ("glu" ,glu)
 324        ("hdf5" ,hdf5)
 325        ("jpeg" ,libjpeg-turbo)
 326        ("jsoncpp" ,jsoncpp)
 327        ("libtheora" ,libtheora)
 328        ("libX11" ,libx11)
 329        ("libxml2" ,libxml2)
 330        ("libXt" ,libxt)
 331        ("lz4" ,lz4)
 332        ("mesa" ,mesa)
 333        ("netcdf" ,netcdf)
 334        ("png" ,libpng)
 335        ("proj" ,proj)
 336        ("python", python)
 337        ;("pugixml" ,pugixml)
 338        ("sqlite" ,sqlite)
 339        ("tiff" ,libtiff)
 340        ("xorgproto" ,xorgproto)
 341        ("zlib" ,zlib)))
 342     (propagated-inputs
 343      ;; VTK's 'VTK-vtk-module-find-packages.cmake' calls
 344      ;; 'find_package(THEORA)', which in turns looks for libogg.
 345      (list libogg))
 346     (home-page "https://vtk.org/")
 347     (synopsis "Libraries for 3D computer graphics")
 348     (description
 349      "The Visualization Toolkit (VTK) is a C++ library for 3D computer graphics,
 350 image processing and visualization.  It supports a wide variety of
 351 visualization algorithms including: scalar, vector, tensor, texture, and
 352 volumetric methods; and advanced modeling techniques such as: implicit
 353 modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay
 354 triangulation.  VTK has an extensive information visualization framework, has
 355 a suite of 3D interaction widgets, supports parallel processing, and
 356 integrates with various databases on GUI toolkits such as Qt and Tk.")
 357     (license license:bsd-3)))
 358
 359 ;; itksnap needs an older variant of VTK.
 360 (define-public vtk-6
 361   (package (inherit vtk)
 362     (version "6.3.0")
 363     (source (origin
 364               (method url-fetch)
 365               (uri (string-append "https://vtk.org/files/release/"
 366                                   (version-major+minor version)
 367                                   "/VTK-" version ".tar.gz"))
 368               (sha256
 369                (base32
 370                 "0pla1r5mvkgl4sl213gfdhzrypdgai0h3z5mfgm6p9jz9hsr794j"))))
 371     (inputs
 372      (modify-inputs (package-inputs vtk)
 373        (replace "jsoncpp" jsoncpp-for-tensorflow)))))
 374
 375 (define-public opencv
 376   (package
 377     (name "opencv")
 378     (version "3.4.3")
 379     (source (origin
 380               (method git-fetch)
 381               (uri (git-reference
 382                      (url "https://github.com/opencv/opencv")
 383                      (commit version)))
 384               (file-name (git-file-name name version))
 385               (sha256
 386                (base32
 387                 "06bc61r8myym4s8im10brdjfg4wxkrvsbhhl7vr1msdan2xddzi3"))
 388               (patches
 389                (search-patches "opencv-fix-build-of-grfmt_jpeg2000.cpp.patch"))
 390               (modules '((guix build utils)))
 391               (snippet
 392                '(begin
 393                   ;; Remove external libraries. We have all available in Guix:
 394                   (delete-file-recursively "3rdparty")
 395
 396                   ;; Milky icon set is non-free:
 397                   (delete-file-recursively "modules/highgui/src/files_Qt/Milky")
 398
 399                   ;; Some jars found:
 400                   (for-each delete-file
 401                             '("modules/java/test/pure_test/lib/junit-4.11.jar"
 402                               "samples/java/sbt/sbt/sbt-launch.jar"))
 403                   #t))))
 404     (build-system cmake-build-system)
 405     (arguments
 406      `(#:configure-flags
 407        (list "-DWITH_IPP=OFF"
 408              "-DWITH_ITT=OFF"
 409              "-DWITH_CAROTENE=OFF" ; only visible on arm/aarch64
 410              "-DENABLE_PRECOMPILED_HEADERS=OFF"
 411
 412              ;; CPU-Features:
 413              ;; See cmake/OpenCVCompilerOptimizations.cmake
 414              ;; (CPU_ALL_OPTIMIZATIONS) for a list of all optimizations
 415              ;; BASELINE is the minimum optimization all CPUs must support
 416              ;;
 417              ;; DISPATCH is the list of optional dispatches.
 418              "-DCPU_BASELINE=SSE2"
 419
 420              ,@(match (%current-system)
 421                  ("x86_64-linux"
 422                   '("-DCPU_DISPATCH=NEON;VFPV3;FP16;SSE;SSE2;SSE3;SSSE3;SSE4_1;SSE4_2;POPCNT;AVX;FP16;AVX2;FMA3;AVX_512F;AVX512_SKX"
 423                     "-DCPU_DISPATCH_REQUIRE=SSE3,SSSE3,SSE4_1,SSE4_2,AVX,AVX2"))
 424                  ("armhf-linux"
 425                   '("-DCPU_BASELINE_DISABLE=NEON")) ; causes build failures
 426                  ("aarch64-linux"
 427                   '("-DCPU_BASELINE=NEON"
 428                     "-DCPU_DISPATCH=NEON;VFPV3;FP16"))
 429                  (_ '()))
 430
 431              "-DBUILD_PERF_TESTS=OFF"
 432              "-DBUILD_TESTS=ON"
 433
 434              (string-append "-DOPENCV_EXTRA_MODULES_PATH=" (getcwd)
 435                             "/opencv-contrib/modules")
 436
 437              ;;Define test data:
 438              (string-append "-DOPENCV_TEST_DATA_PATH=" (getcwd)
 439                             "/opencv-extra/testdata")
 440
 441              ;; Is ON by default and would try to rebuild 3rd-party protobuf,
 442              ;; which we had removed, which would lead to an error:
 443              "-DBUILD_PROTOBUF=OFF"
 444
 445              ;; Rebuild protobuf files, because we have a slightly different
 446              ;; version than the included one. If we would not update, we
 447              ;; would get a compile error later:
 448              "-DPROTOBUF_UPDATE_FILES=ON"
 449
 450              ;; xfeatures2d disabled, because it downloads extra binaries from
 451              ;; https://github.com/opencv/opencv_3rdparty
 452              ;; defined in xfeatures2d/cmake/download_{vgg|bootdesc}.cmake
 453              ;; Cmp this bug entry:
 454              ;; https://github.com/opencv/opencv_contrib/issues/1131
 455              "-DBUILD_opencv_xfeatures2d=OFF")
 456        #:phases
 457        (modify-phases %standard-phases
 458          (add-after 'unpack 'disable-broken-tests
 459            (lambda _
 460              ;; These tests fails with:
 461              ;; vtkXOpenGLRenderWindow (0x723990): Could not find a decent config
 462              ;; I think we have no OpenGL support with the Xvfb.
 463              (substitute* '("modules/viz/test/test_tutorial3.cpp"
 464                             "modules/viz/test/test_main.cpp"
 465                             "modules/viz/test/tests_simple.cpp"
 466                             "modules/viz/test/test_viz3d.cpp")
 467                (("(TEST\\(Viz, )([a-z].*\\).*)" all pre post)
 468                 (string-append pre "DISABLED_" post)))
 469
 470              ;; This one fails with "unknown file: Failure"
 471              ;; But I couldn't figure out which file was missing:
 472              (substitute* "../opencv-contrib/modules/face/test/test_face_align.cpp"
 473                (("(TEST\\(CV_Face_FacemarkKazemi, )(can_detect_landmarks\\).*)"
 474                  all pre post)
 475                 (string-append pre "DISABLED_" post)))
 476
 477              ;; Failure reason: Bad accuracy
 478              ;; Incorrect count of accurate poses [2nd case]: 90.000000 / 94.000000
 479              (substitute* "../opencv-contrib/modules/rgbd/test/test_odometry.cpp"
 480                (("(TEST\\(RGBD_Odometry_Rgbd, )(algorithmic\\).*)" all pre post)
 481                 (string-append pre "DISABLED_" post)))
 482              #t))
 483
 484          (add-after 'unpack 'unpack-submodule-sources
 485            (lambda* (#:key inputs #:allow-other-keys)
 486              (mkdir "../opencv-extra")
 487              (mkdir "../opencv-contrib")
 488              (copy-recursively (assoc-ref inputs "opencv-extra")
 489                                "../opencv-extra")
 490              (copy-recursively (assoc-ref inputs "opencv-contrib")
 491                                "../opencv-contrib")))
 492
 493          (add-after 'set-paths 'add-ilmbase-include-path
 494            (lambda* (#:key inputs #:allow-other-keys)
 495            ;; OpenEXR propagates ilmbase, but its include files do not appear
 496            ;; in the CPATH, so we need to add "$ilmbase/include/OpenEXR/" to
 497            ;; the CPATH to satisfy the dependency on "ImathVec.h".
 498            (setenv "CPATH"
 499                    (string-append
 500                     (string-drop-right
 501                      (search-input-file inputs "include/OpenEXR/ImathVec.h")
 502                      11)
 503                     ":" (or (getenv "CPATH") "")))))
 504        (add-before 'check 'start-xserver
 505          (lambda* (#:key inputs #:allow-other-keys)
 506            (let ((xorg-server (assoc-ref inputs "xorg-server"))
 507                  (disp ":1"))
 508              (setenv "HOME" (getcwd))
 509              (setenv "DISPLAY" disp)
 510              ;; There must be a running X server and make check doesn't start one.
 511              ;; Therefore we must do it.
 512              (zero? (system (format #f "~a/bin/Xvfb ~a &" xorg-server disp)))))))))
 513     (native-inputs
 514      `(("pkg-config" ,pkg-config)
 515        ("xorg-server" ,xorg-server-for-tests) ; For running the tests
 516        ("opencv-extra"
 517         ,(origin
 518            (method git-fetch)
 519            (uri (git-reference
 520                   (url "https://github.com/opencv/opencv_extra")
 521                   (commit version)))
 522            (file-name (git-file-name "opencv_extra" version))
 523            (sha256
 524             (base32 "08p5xnq8n1jw8svvz0fnirfg7q8dm3p4a5dl7527s5xj0f9qn7lp"))))
 525        ("opencv-contrib"
 526         ,(origin
 527            (method git-fetch)
 528            (uri (git-reference
 529                   (url "https://github.com/opencv/opencv_contrib")
 530                   (commit version)))
 531            (file-name (git-file-name "opencv_contrib" version))
 532            (patches (search-patches "opencv-rgbd-aarch64-test-fix.patch"))
 533            (sha256
 534             (base32 "1f334glf39nk42mpqq6j732h3ql2mpz89jd4mcl678s8n73nfjh2"))))))
 535     (inputs `(("libjpeg" ,libjpeg-turbo)
 536               ("libpng" ,libpng)
 537               ("jasper" ,jasper)
 538               ;; ffmpeg 4.0 causes core dumps in tests.
 539               ("ffmpeg" ,ffmpeg-3.4)
 540               ("libtiff" ,libtiff)
 541               ("hdf5" ,hdf5)
 542               ("libgphoto2" ,libgphoto2)
 543               ("libwebp" ,libwebp)
 544               ("zlib" ,zlib)
 545               ("gtkglext" ,gtkglext)
 546               ("openexr" ,openexr-2)
 547               ("ilmbase" ,ilmbase)
 548               ("gtk+" ,gtk+-2)
 549               ("python-numpy" ,python-numpy)
 550               ("protobuf" ,protobuf)
 551               ("vtk" ,vtk)
 552               ("python" ,python)))
 553     ;; These three CVEs are not a problem of OpenCV, see:
 554     ;; https://github.com/opencv/opencv/issues/10998
 555     (properties '((lint-hidden-cve . ("CVE-2018-7712"
 556                                       "CVE-2018-7713"
 557                                       "CVE-2018-7714"))))
 558     (synopsis "Computer vision library")
 559     (description "OpenCV is a library aimed at
 560 real-time computer vision, including several hundred computer
 561 vision algorithms.  It can be used to do things like:
 562
 563 @itemize
 564 @item image and video input and output
 565 @item image and video processing
 566 @item displaying
 567 @item feature recognition
 568 @item segmentation
 569 @item facial recognition
 570 @item stereo vision
 571 @item structure from motion
 572 @item augmented reality
 573 @item machine learning
 574 @end itemize\n")
 575     (home-page "https://opencv.org/")
 576     (license license:bsd-3)))
 577
 578 (define-public vips
 579   (package
 580     (name "vips")
 581     (version "8.10.6")
 582     (source
 583      (origin
 584        (method url-fetch)
 585        (uri (string-append
 586              "https://github.com/libvips/libvips/releases/download/v"
 587              version "/vips-" version ".tar.gz"))
 588        (sha256
 589         (base32 "0vjsh3i0861f6h9as3bch956cidz824zz499pvhjs3lfjn6hhs14"))))
 590     (build-system gnu-build-system)
 591     (native-inputs
 592      (list gobject-introspection pkg-config))
 593     (inputs
 594      (list expat
 595            fftw
 596            giflib
 597            glib
 598            hdf5
 599            imagemagick
 600            lcms
 601            libexif
 602            libgsf
 603            libjpeg-turbo
 604            libpng
 605            librsvg
 606            libtiff
 607            libxml2
 608            libwebp
 609            matio
 610            niftilib
 611            openexr-2
 612            orc
 613            pango
 614            poppler))
 615     (home-page "https://libvips.github.io/libvips/")
 616     (synopsis "Multithreaded image processing system with low memory needs")
 617     (description
 618      "VIPS is a demand-driven, horizontally threaded image processing library.
 619 It's particularly good at processing large images, working with colour,
 620 scientific analysis, and general research & development.
 621
 622 Compared to most image processing libraries VIPS needs little RAM and runs
 623 quickly, especially on machines with more than one CPU core.  This is primarily
 624 due to its architecture which automatically parallelises the image workflows.")
 625     (license license:lgpl2.1+)))
 626
 627 (define-public gmic
 628   (package
 629     (name "gmic")
 630     (version "2.9.7")
 631     (source
 632      (origin
 633        (method url-fetch)
 634        (uri (string-append "https://gmic.eu/files/source/gmic_"
 635                            version ".tar.gz"))
 636        (sha256
 637         (base32 "05kzaplsl5qvxs7v6g73q0lq8dii8g6v77ap609188m7gr43f9cl"))))
 638     (build-system cmake-build-system)
 639     (arguments
 640      `(#:tests? #f ;there are no tests
 641        #:configure-flags '("-DBUILD_LIB_STATIC=OFF"
 642                            "-DENABLE_DYNAMIC_LINKING=ON"
 643                            "-DENABLE_LTO=ON")
 644        #:phases
 645        (modify-phases %standard-phases
 646          (add-before 'configure 'set-LDFLAGS
 647            (lambda* (#:key inputs outputs #:allow-other-keys)
 648              (setenv "LDFLAGS"
 649                      (string-append
 650                       "-Wl,-rpath="
 651                       (assoc-ref outputs "out") "/lib")))))))
 652     (native-inputs
 653      (list pkg-config))
 654     (inputs
 655      (list curl
 656            fftw
 657            graphicsmagick
 658            libjpeg-turbo
 659            libpng
 660            libtiff
 661            libx11
 662            ;;("opencv" ,opencv) ;OpenCV is currently broken in the CI
 663            openexr-2
 664            zlib))
 665     (home-page "https://gmic.eu/")
 666     (synopsis "Full-featured framework for digital image processing")
 667     (description "G'MIC is a full-featured framework for digital image
 668 processing.  It provides several user interfaces to convert / manipulate
 669 / filter / visualize generic image datasets, ranging from 1D scalar
 670 signals to 3D+t sequences of multi-spectral volumetric images, hence
 671 including 2D color images.")
 672     ;; Dual-licensed, either license applies.
 673     (license (list license:cecill license:cecill-c))))
 674
 675 (define-public gmic-qt
 676   (package
 677     (inherit gmic)
 678     (name "gmic-qt")
 679     (arguments
 680      (substitute-keyword-arguments (package-arguments gmic)
 681        ((#:configure-flags _)
 682         `(list "-DGMIC_QT_HOST=none" "-DENABLE_DYNAMIC_LINKING=ON"
 683                (string-append "-DGMIC_LIB_PATH="
 684                               (assoc-ref %build-inputs "gmic") "/lib")))
 685         ((#:phases phases)
 686          `(modify-phases ,phases
 687             (add-after 'unpack 'qt-chdir
 688               (lambda _ (chdir "gmic-qt") #t))))))
 689     (native-inputs
 690      (list pkg-config qttools))
 691     (inputs
 692      (modify-inputs (package-inputs gmic)
 693        (prepend gmic qtbase-5)))
 694     (synopsis "Qt frontend for the G'MIC image processing framework")
 695     (license license:gpl3+)))
 696
 697 (define-public gmic-qt-krita
 698   (package
 699     (inherit gmic-qt)
 700     (name "gmic-qt-krita")
 701     (arguments
 702      (substitute-keyword-arguments (package-arguments gmic-qt)
 703        ((#:configure-flags flags)
 704         '(list "-DGMIC_QT_HOST=krita" "-DENABLE_DYNAMIC_LINKING=ON"
 705                (string-append "-DGMIC_LIB_PATH="
 706                               (assoc-ref %build-inputs "gmic") "/lib")))))
 707     (synopsis "Krita plugin for the G'MIC image processing framework")))
 708
 709 (define-public gmic-qt-gimp
 710   (package
 711     (inherit gmic-qt)
 712     (name "gmic-qt-gimp")
 713     (inputs
 714      ;; GIMP and its dependencies.
 715      (modify-inputs (package-inputs gmic-qt)
 716        (prepend gimp gdk-pixbuf cairo gegl)))
 717     (arguments
 718      (substitute-keyword-arguments (package-arguments gmic-qt)
 719        ((#:configure-flags flags)
 720         '(list "-DGMIC_QT_HOST=gimp" "-DENABLE_DYNAMIC_LINKING=ON"
 721                (string-append "-DGMIC_LIB_PATH="
 722                               (assoc-ref %build-inputs "gmic") "/lib")))))
 723     (synopsis "GIMP plugin for the G'MIC image processing framework")))
 724
 725 (define-public nip2
 726   (package
 727     (name "nip2")
 728     (version "8.7.1")
 729     (source
 730      (origin
 731        (method url-fetch)
 732        (uri (string-append "https://github.com/libvips/nip2/releases/download/v"
 733                            version "/nip2-" version ".tar.gz" ))
 734        (sha256
 735         (base32 "0l7n427njif53npqn02gfjjly8y3khbrkzqxp10j5vp9h97psgiw"))))
 736     (build-system gnu-build-system)
 737     (arguments
 738      `(#:phases
 739        (modify-phases %standard-phases
 740          ;; test_conv.ws keep failing so disabling for now.
 741          (add-after 'unpack 'disable-test-conv
 742            (lambda _
 743              (delete-file "test/workspaces/test_conv.ws")
 744              #t))
 745          (add-before 'check 'set-home
 746            (lambda _
 747              (setenv "HOME" "/tmp") #t)))))
 748     (inputs
 749      `(("vips" ,vips)
 750        ("glib" ,glib)
 751        ("libtiff" ,libtiff)
 752        ("gtk+-2" ,gtk+-2)
 753        ("libxml2" ,libxml2)
 754        ("libexif" ,libexif)
 755        ("libjpeg" ,libjpeg-turbo)        ;required by vips.pc
 756        ("librsvg" ,librsvg)
 757        ("fftw" ,fftw)
 758        ("libgsf" ,libgsf)
 759        ("imagemagick" ,imagemagick)
 760        ("orc" ,orc)
 761        ("matio" ,matio)
 762        ("lcms" ,lcms)
 763        ("libwebp" ,libwebp)
 764        ("openexr" ,openexr-2)
 765        ("poppler" ,poppler)
 766        ("gsl" ,gsl)))
 767     (native-inputs
 768      (list flex bison 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      (list libgeotiff libtiff libjpeg-turbo libpng zlib))
 809     (home-page "https://github.com/vxl/vxl/")
 810     (synopsis "Collection of C++ libraries for computer vision")
 811     (description "VXL (the Vision-something-Libraries) is a collection of C++
 812 libraries designed for computer vision research and implementation.")
 813     (license license:bsd-3)))
 814
 815 (define-public vxl-1
 816   (package (inherit vxl)
 817     (name "vxl")
 818     (version "1.18.0")
 819     (source
 820      (origin
 821        (method git-fetch)
 822        (uri (git-reference
 823              (url "https://github.com/vxl/vxl")
 824              (commit (string-append "v" version))))
 825        (file-name (git-file-name name version))
 826        (sha256
 827         (base32 "1g4mr2cc58jwm0vasscbd4y5380wj3ahkvq121z4gs83fhavvxgz"))
 828        (modules '((guix build utils)))
 829        (snippet
 830         '(begin
 831            (for-each delete-file-recursively
 832                      '("v3p/bzlib/"
 833                        "v3p/geotiff/"
 834                        "v3p/png/"
 835                        "v3p/tiff/"
 836                        "v3p/zlib/"))
 837            (substitute* "v3p/CMakeLists.txt"
 838              (("add_subdirectory\\((tiff|png|jpeg|zlib|bzlib|geotiff)\\)")
 839               ""))
 840            #t))))
 841     (arguments
 842      `(#:configure-flags
 843        ;; Needed for itk-snap
 844        (list "-DVNL_CONFIG_LEGACY_METHODS=ON")))))
 845
 846 (define-public insight-toolkit
 847   (package
 848     (name "insight-toolkit")
 849     (version "5.0.0")
 850     (source
 851      (origin
 852        (method url-fetch)
 853        (uri (string-append "https://github.com/InsightSoftwareConsortium/ITK/"
 854                            "releases/download/v" version "/InsightToolkit-"
 855                            version ".tar.xz"))
 856        (sha256
 857         (base32 "0bs63mk4q8jmx38f031jy5w5n9yy5ng9x8ijwinvjyvas8cichqi"))))
 858     (build-system cmake-build-system)
 859     (arguments
 860      `(#:tests? #f            ; tests require network access and external data
 861        #:configure-flags
 862        '("-DITK_USE_GPU=ON"
 863          "-DITK_USE_SYSTEM_LIBRARIES=ON"
 864          "-DITK_USE_SYSTEM_GOOGLETEST=ON"
 865          "-DITK_BUILD_SHARED=ON"
 866          ;; This prevents "GTest::GTest" from being added to the ITK_LIBRARIES
 867          ;; variable in the installed CMake files.  This is necessary as other
 868          ;; packages using insight-toolkit could not be configured otherwise.
 869          "-DGTEST_ROOT=gtest")
 870
 871        #:phases
 872        (modify-phases %standard-phases
 873          (add-after 'unpack 'do-not-tune
 874            (lambda _
 875              (substitute* "CMake/ITKSetStandardCompilerFlags.cmake"
 876                (("-mute=native") ""))
 877              #t)))))
 878     (inputs
 879      `(("eigen" ,eigen)
 880        ("expat" ,expat)
 881        ("fftw" ,fftw)
 882        ("fftwf" ,fftwf)
 883        ("hdf5" ,hdf5)
 884        ("libjpeg" ,libjpeg-turbo)
 885        ("libpng" ,libpng)
 886        ("libtiff" ,libtiff)
 887        ("mesa" ,mesa-opencl)
 888        ("perl" ,perl)
 889        ("python" ,python)
 890        ("tbb" ,tbb)
 891        ("vxl" ,vxl-1)
 892        ("zlib" ,zlib)))
 893     (native-inputs
 894      (list googletest pkg-config))
 895     (home-page "https://github.com/InsightSoftwareConsortium/ITK/")
 896     (synopsis "Scientific image processing, segmentation and registration")
 897     (description "The Insight Toolkit (ITK) is a toolkit for N-dimensional
 898 scientific image processing, segmentation, and registration.  Segmentation is
 899 the process of identifying and classifying data found in a digitally sampled
 900 representation.  Typically the sampled representation is an image acquired
 901 from such medical instrumentation as CT or MRI scanners.  Registration is the
 902 task of aligning or developing correspondences between data.  For example, in
 903 the medical environment, a CT scan may be aligned with a MRI scan in order to
 904 combine the information contained in both.")
 905     (license license:asl2.0)))
 906
 907 (define-public insight-toolkit-4
 908   (package (inherit insight-toolkit)
 909     (version "4.13.2")
 910     (source
 911      (origin
 912        (method url-fetch)
 913        (uri (string-append "https://github.com/InsightSoftwareConsortium/ITK/"
 914                            "releases/download/v" version "/InsightToolkit-"
 915                            version ".tar.xz"))
 916        (sha256
 917         (base32 "19cgfpd63gqrvc3m27m394gy2d7w79g5y6lvznb5qqr49lihbgns"))))
 918     (arguments
 919      `(#:tests? #f            ; tests require network access and external data
 920        #:configure-flags
 921        '("-DITKV3_COMPATIBILITY=ON"     ; needed for itk-snap
 922          "-DITK_USE_GPU=ON"
 923          "-DITK_USE_SYSTEM_LIBRARIES=ON"
 924          "-DITK_USE_SYSTEM_GOOGLETEST=ON"
 925          "-DITK_USE_SYSTEM_VXL=ON")))))
 926
 927 (define-public insight-toolkit-4.12
 928   (package (inherit insight-toolkit-4)
 929     (version "4.12.2")
 930     (source
 931      (origin
 932        (method url-fetch)
 933        (uri (string-append "mirror://sourceforge/itk/itk/4.12/"
 934                            "InsightToolkit-" version ".tar.xz"))
 935        (sha256
 936         (base32 "1qw9mxbh083siljygahl4gdfv91xvfd8hfl7ghwii19f60xrvn2w"))))))
 937
 938 (define-public itk-snap
 939   (package
 940     (name "itk-snap")
 941     (version "3.8.0")
 942     (source
 943      (origin
 944        (method git-fetch)
 945        (uri (git-reference
 946              (url "https://git.code.sf.net/p/itk-snap/src")
 947              (commit (string-append "v" version))))
 948        (file-name (git-file-name name version))
 949        (sha256
 950         (base32 "15i5ixpryfrbf3vrrb5rici8fb585f25k0v1ljds16bp1f1msr4q"))))
 951     (build-system cmake-build-system)
 952     (arguments
 953      `(#:configure-flags
 954        (list "-DSNAP_VERSION_GIT_SHA1=release"
 955              "-DSNAP_VERSION_GIT_BRANCH=release"
 956              "-DSNAP_VERSION_GIT_TIMESTAMP=0"
 957              "-DSNAP_PACKAGE_QT_PLUGINS=OFF"
 958              "-DCMAKE_POSITION_INDEPENDENT_CODE=ON")
 959        #:phases
 960        (modify-phases %standard-phases
 961          ;; During the installation phase all libraries provided by all
 962          ;; dependencies will be copied to the lib directory.  That's insane,
 963          ;; so we disable this.
 964          (add-after 'unpack 'do-not-copy-dependencies
 965            (lambda _
 966              (substitute* "CMakeLists.txt"
 967                (("install_qt5_executable\
 968 \\(\\$\\{SNAP_MAIN_INSTALL_DIR\\}/\\$\\{SNAP_EXE\\}\\)")
 969                 ""))
 970              #t))
 971          (add-after 'unpack 'disable-gui-tests
 972            (lambda _
 973              ;; The GUI tests just time out.
 974              (substitute* "CMakeLists.txt"
 975                (("  (Workspace|DiffSpace|ProbeIntensity|RegionCompetition\
 976 |RandomForest|RandomForestBailOut)")
 977                 ""))
 978              #t))
 979          (add-after 'unpack 'make-reproducible
 980            (lambda _
 981              (substitute* "CMakeLists.txt"
 982                (("TODAY\\(SNAP_VERSION_COMPILE_DATE\\)")
 983                 "SET(SNAP_VERSION_COMPILE_DATE \"(removed for reproducibility)\")"))
 984              #t))
 985          (add-after 'unpack 'prepare-submodules
 986            (lambda* (#:key inputs #:allow-other-keys)
 987              (rmdir "Submodules/c3d")
 988              (copy-recursively (assoc-ref inputs "c3d-src")
 989                                "Submodules/c3d")
 990              (substitute* '("Submodules/c3d/adapters/BiasFieldCorrectionN4.cxx"
 991                             "Submodules/c3d/adapters/ApplyMetric.cxx")
 992                (("vcl_") "std::"))
 993              (rmdir "Submodules/greedy")
 994              (symlink (assoc-ref inputs "greedy-src")
 995                       "Submodules/greedy")
 996              #t))
 997          (add-after 'unpack 'fix-includes
 998            (lambda _
 999              (substitute* "GUI/Model/RegistrationModel.cxx"
1000                (("<vnl_symmetric_eigensystem.h>")
1001                 "<vnl/algo/vnl_symmetric_eigensystem.h>"))
1002              #t))
1003          (add-before 'check 'prepare-tests
1004            (lambda _
1005              ;; Needed by at least one test.
1006              (setenv "HOME" "/tmp")
1007              #t))
1008          (add-after 'install 'wrap-executable
1009            (lambda* (#:key inputs outputs #:allow-other-keys)
1010              (let ((out (assoc-ref outputs "out")))
1011                (wrap-program (string-append out "/bin/itksnap")
1012                  `("QT_PLUGIN_PATH" ":" prefix
1013                    ,(map (lambda (label)
1014                            (string-append (assoc-ref inputs label)
1015                                           "/lib/qt5/plugins"))
1016                          '("qtbase" "qtdeclarative"))))
1017                #t))))))
1018     (inputs
1019      `(("curl" ,curl)
1020        ("fftw" ,fftw)
1021        ("fftwf" ,fftwf)
1022        ("glu" ,glu)
1023        ("hdf5" ,hdf5)
1024        ("mesa" ,mesa-opencl)
1025        ;; This package does not build with either insight-toolkit 5.0.0 and
1026        ;; not with 4.13.  It really needs to be 4.12.
1027        ("itk" ,insight-toolkit-4.12)
1028        ("vtk" ,vtk-6)
1029        ("qtbase" ,qtbase-5)
1030        ("qtdeclarative" ,qtdeclarative)
1031        ("vxl" ,vxl-1)
1032        ("zlib" ,zlib)))
1033     (native-inputs
1034      `(("googletest" ,googletest)
1035        ("qttools" ,qttools)
1036        ("pkg-config" ,pkg-config)
1037        ("c3d-src"
1038         ,(let* ((commit "f521358db26e00002c911cc47bf463b043942ad3")
1039                 (revision "1")
1040                 (version (git-version "0" revision commit)))
1041            (origin
1042              (method git-fetch)
1043              (uri (git-reference
1044                    (url "https://github.com/pyushkevich/c3d")
1045                    (commit commit)))
1046              (file-name (git-file-name "c3d" version))
1047              (sha256
1048               (base32
1049                "0kyv3rxrxwr8c3sa9zv01lsnhk95b27gx1s870k3yi8qp52h7bx3")))))
1050        ;; We are using an arbitrary commit from 2017 because the latest
1051        ;; version breaks the build...
1052        ("greedy-src"
1053         ,(let* ((commit "97e340f7e8e66597599144947775e6039e79a0d3")
1054                 (revision "1")
1055                 (version (git-version "0" revision commit)))
1056            (origin
1057              (method git-fetch)
1058              (uri (git-reference
1059                    (url "https://github.com/pyushkevich/greedy")
1060                    (commit commit)))
1061              (file-name (git-file-name "greedy" version))
1062              (sha256
1063               (base32
1064                "0k5bc9za4jrc8z9dj08z1rkcp5xf0gnd1d2jmi1w9ny4vxh2q2ab")))))))
1065     (home-page "https://sourceforge.net/p/itk-snap/")
1066     (synopsis "Medical image segmentation")
1067     (description "ITK-SNAP is a tool for segmenting anatomical structures in
1068 medical images.  It provides an automatic active contour segmentation
1069 pipeline, along with supporting a manual segmentation toolbox.  ITK-SNAP has a
1070 full-featured UI aimed at clinical researchers.")
1071     ;; This includes the submodules greedy and c3d.
1072     (license license:gpl3+)))
1073
1074 (define-public metapixel
1075   ;; Follow stable branch.
1076   (let ((commit "98ee9daa093b6c334941242e63f90b1c2876eb4f"))
1077     (package
1078       (name "metapixel")
1079       (version (git-version "1.0.2" "1" commit))
1080       (source
1081        (origin
1082          (method git-fetch)
1083          (uri (git-reference
1084                (url "https://github.com/schani/metapixel")
1085                (commit commit)
1086                ;; TODO: Package rwimg and lispreader?
1087                (recursive? #t)))
1088          (file-name (git-file-name name version))
1089          (sha256
1090           (base32 "0r7n3a6bvcxkbpda4mwmrpicii09iql5z69nkjqygkwxw7ny3309"))))
1091       (build-system gnu-build-system)
1092       (inputs
1093        `(("giflib" ,giflib)
1094          ("libjpeg" ,libjpeg-turbo)
1095          ("libpng" ,libpng)
1096          ("perl" ,perl)))
1097       (native-inputs
1098        `(("pkg-config" ,pkg-config)
1099          ("docbook-xml" ,docbook-xml)
1100          ("docbook-xsl" ,docbook-xsl)
1101          ("xsltproc" ,libxslt)))
1102       (arguments
1103        `(#:tests? #f                    ; No tests.
1104          #:make-flags (list
1105                        (string-append "PREFIX=" (assoc-ref %outputs "out"))
1106                        (string-append "MANPAGE_XSL="
1107                                       (assoc-ref %build-inputs "docbook-xsl")
1108                                       "/xml/xsl/docbook-xsl-*/manpages/docbook.xsl"))
1109          #:phases
1110          (modify-phases %standard-phases
1111            (delete 'configure)
1112            (add-before 'install 'make-local-docbook-xml
1113              (lambda* (#:key inputs #:allow-other-keys)
1114                (substitute* "metapixel.xml"
1115                  (("http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd")
1116                   (string-append (assoc-ref inputs "docbook-xml")
1117                                  "/xml/dtd/docbook/docbookx.dtd")))
1118                #t))
1119            (add-before 'install 'fix-directory-creation
1120              (lambda* (#:key outputs #:allow-other-keys)
1121                (mkdir-p (string-append (assoc-ref outputs "out") "/share/man/man1"))
1122                #t)))))
1123       (home-page "https://www.complang.tuwien.ac.at/schani/metapixel/")
1124       (synopsis "Photomosaics generator")
1125       (description "Metapixel is a program for generating photomosaics.  It can
1126 generate classical photomosaics, in which the source image is viewed as a
1127 matrix of equally sized rectangles for each of which a matching image is
1128 substituted, as well as collage-style photomosaics, in which rectangular parts
1129 of the source image at arbitrary positions (i.e. not aligned to a matrix) are
1130 substituted by matching images.")
1131       (license license:gpl2))))
1132
1133 (define-public scantailor-advanced
1134   (let ((commit "3d1e74e6ace413733511086934a66f4e3f7a6027"))
1135     (package
1136       (name "scantailor-advanced")
1137       (version (string-append "1.0.16-" (string-take commit 7)))
1138       (source
1139        (origin
1140          (method git-fetch)
1141          (uri (git-reference
1142                (url "https://github.com/4lex4/scantailor-advanced")
1143                (commit commit)))
1144          (file-name (git-file-name name version))
1145          (sha256
1146           (base32
1147            "0kixwjb2x457dq7927hkh34c803p7yh1pmn6n61rk9shqrcg492h"))))
1148       (build-system qt-build-system)
1149       (native-inputs
1150        (list qttools))
1151       (inputs
1152        `(("boost" ,boost)
1153          ("libjpeg" ,libjpeg-turbo)
1154          ("libpng" ,libpng)
1155          ("libtiff" ,libtiff)
1156          ("qtbase" ,qtbase-5)
1157          ("qtsvg" ,qtsvg)
1158          ("zlib" ,zlib)))
1159       (arguments
1160        `(#:phases
1161          (modify-phases %standard-phases
1162            ;; Some tests require a display and fail with offscreen mode.
1163            (add-after 'unpack 'disable-failing-tests
1164              (lambda _
1165                (setenv "ARGS" "--exclude-regex \"imageproc_.*\"")
1166                #t)))))
1167       (home-page "https://github.com/4lex4/scantailor-advanced")
1168       (synopsis "Clean up scanned pages")
1169       (description "Scan Tailor is an interactive post-processing tool for
1170 scanned pages.  It performs operations such as page splitting, deskewing,
1171 adding/removing borders, and others.  You give it raw scans, and you get pages
1172 ready to be printed or assembled into a PDF or DJVU file.  Scanning, optical
1173 character recognition, and assembling multi-page documents are out of scope of
1174 this project.
1175
1176 Scan Tailer Advanced is a fork of Scan Tailer that merges Scan Tailor Featured
1177 and Scan Tailor Enhanced versions as well as including many more bug fixes.")
1178       (license license:gpl3+))))
1179
1180 (define-public stiff
1181   (package
1182     (name "stiff")
1183     (version "2.4.0")
1184     (source
1185      (origin
1186        (method url-fetch)
1187        (uri (string-append "https://www.astromatic.net/download/stiff/stiff-"
1188                            version ".tar.gz"))
1189        (sha256
1190         (base32 "14m92dskzw7bwsr64ha4p0mj3ndv13gwcbfic3qxrs3zq5353s7l"))))
1191     (build-system gnu-build-system)
1192     (inputs
1193      (list libtiff zlib libjpeg-turbo))
1194     (home-page "https://www.astromatic.net/software/stiff")
1195     (synopsis "Convert scientific FITS images to TIFF format")
1196     (description
1197      "STIFF is a program that converts scientific @acronym{FITS, Flexible Image
1198 Transport System} images to the more popular TIFF format for illustration
1199 purposes.")
1200     (license license:gpl3+)))
1201
1202 (define-public python-imgviz
1203   (package
1204     (name "python-imgviz")
1205     (version "1.2.6")
1206     (source
1207      (origin
1208        ;; PyPi tarball lacks tests.
1209        (method git-fetch)
1210        (uri (git-reference
1211              (url "https://github.com/wkentaro/imgviz.git")
1212              (commit (string-append "v" version))))
1213        (file-name (git-file-name name version))
1214        (sha256
1215         (base32 "1bm0wdv5p26i8nl4kx3145cz553v401sgbpgc96sddzjfmfiydcw"))))
1216     (build-system python-build-system)
1217     (arguments
1218      `(#:phases
1219        (modify-phases %standard-phases
1220          (replace 'check
1221            (lambda* (#:key inputs outputs tests? #:allow-other-keys)
1222              (when tests?
1223                (add-installed-pythonpath inputs outputs)
1224                (invoke "pytest" "-v" "tests"))
1225              #t)))))
1226     (propagated-inputs
1227       (list python-matplotlib python-numpy python-pillow python-pyyaml))
1228     (native-inputs (list python-pytest))
1229     (home-page "http://github.com/wkentaro/imgviz")
1230     (synopsis "Image Visualization Tools")
1231     (description "Python library for object detection, semantic and instance
1232 segmentation.")
1233     (license license:expat)))
1234
1235 (define-public labelme
1236   (package
1237     (name "labelme")
1238     (version "4.5.13")
1239     (source
1240      (origin
1241        ;; PyPi tarball lacks tests.
1242        (method git-fetch)
1243        (uri (git-reference
1244              (url "https://github.com/wkentaro/labelme.git")
1245              (commit (string-append "v" version))))
1246        (file-name (git-file-name name version))
1247        (sha256
1248         (base32 "0cmi2xb4dgh7738l259rgwhn9l134f0vnaaqc2gflc5yr3lqhrv2"))))
1249     (build-system python-build-system)
1250     (arguments
1251      `(#:phases
1252        (modify-phases %standard-phases
1253          (add-after 'unpack 'loosen-requirements
1254            (lambda _
1255              ;; Don't require an outdated version of matplotlib.
1256              (substitute* "setup.py"
1257                (("matplotlib<3\\.3")
1258                 "matplotlib"))))
1259          (add-before 'check 'start-xserver
1260            (lambda* (#:key inputs #:allow-other-keys)
1261              (let ((xorg-server (assoc-ref inputs "xorg-server")))
1262                ;; Options taken from CI workflow.
1263                (system (string-append xorg-server "/bin/Xvfb :99 -screen 0 "
1264                                       "1920x1200x24 -ac +extension GLX +render "
1265                                       "-noreset &"))
1266                (setenv "DISPLAY" ":99.0"))))
1267          (replace 'check
1268            (lambda* (#:key inputs outputs tests? #:allow-other-keys)
1269              (when tests?
1270                (add-installed-pythonpath inputs outputs)
1271                ;; Fails when invoking help2man for unknown reason.
1272                (delete-file "tests/docs_tests/man_tests/test_labelme_1.py")
1273                ;; One test hangs.
1274                (delete-file "tests/labelme_tests/widgets_tests/test_label_dialog.py")
1275                ;; Calls incompatible function signatures.
1276                (delete-file "tests/labelme_tests/widgets_tests/test_label_list_widget.py")
1277                (setenv "MPLBACKEND" "agg")
1278                (invoke "pytest" "-v" "tests" "-m" "not gpu")))))))
1279     (propagated-inputs
1280       (list python-imgviz
1281             python-matplotlib
1282             python-numpy
1283             python-pillow
1284             python-pyyaml
1285             python-qtpy
1286             python-termcolor))
1287     (native-inputs
1288       (list python-pytest python-pytest-qt xorg-server-for-tests))
1289     (home-page "https://github.com/wkentaro/labelme")
1290     (synopsis
1291       "Image Polygonal Annotation")
1292     (description
1293       "Image and video labeling tool supporting different shapes like
1294 polygons, rectangles, circles, lines, points and VOC/COCO export.")
1295     (license license:gpl3+)))