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