gnu/packages/image-processing.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2017 John Darrington <jmd@gnu.org>
   3 ;;; Copyright © 2017, 2019 Ricardo Wurmus <rekado@elephly.net>
   4 ;;; Copyright © 2014 Ludovic Courtès <ludo@gnu.org>
   5 ;;; Copyright © 2014 Mark H Weaver <mhw@netris.org>
   6 ;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.org>
   7 ;;; Copyright © 2018–2021 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     (build-system cmake-build-system)
 274     (arguments
 275      '(#:build-type "Release"           ;Build without '-g' to save space.
 276        #:configure-flags '(;"-DBUILD_TESTING:BOOL=TRUE"
 277                            ;    ; not honored
 278                            "-DVTK_USE_EXTERNAL=OFF" ;; default
 279                            "-DVTK_MODULE_USE_EXTERNAL_VTK_doubleconversion=ON"
 280                            "-DVTK_MODULE_USE_EXTERNAL_VTK_eigen=ON"
 281                            "-DVTK_MODULE_USE_EXTERNAL_VTK_expat=ON"
 282                            "-DVTK_MODULE_USE_EXTERNAL_VTK_freetype=ON"
 283                            "-DVTK_MODULE_USE_EXTERNAL_VTK_gl2ps=ON"
 284                            "-DVTK_MODULE_USE_EXTERNAL_VTK_glew=ON"
 285                            "-DVTK_MODULE_USE_EXTERNAL_VTK_hdf5=ON"
 286                            "-DVTK_MODULE_USE_EXTERNAL_VTK_jpeg=ON"
 287                            "-DVTK_MODULE_USE_EXTERNAL_VTK_jsoncpp=ON"
 288                            "-DVTK_MODULE_USE_EXTERNAL_VTK_libproj=ON"
 289                            "-DVTK_MODULE_USE_EXTERNAL_VTK_libxml2=ON"
 290                            "-DVTK_MODULE_USE_EXTERNAL_VTK_lz4=ON"
 291                            "-DVTK_MODULE_USE_EXTERNAL_VTK_netcdf=ON"
 292                            "-DVTK_MODULE_USE_EXTERNAL_VTK_ogg=ON"
 293                            "-DVTK_MODULE_USE_EXTERNAL_VTK_png=ON"
 294                            ;"-DVTK_MODULE_USE_EXTERNAL_VTK_pugixml=ON"    ; breaks IO/CityGML
 295                            "-DVTK_MODULE_USE_EXTERNAL_VTK_sqlite=ON"
 296                            "-DVTK_MODULE_USE_EXTERNAL_VTK_theora=ON"
 297                            "-DVTK_MODULE_USE_EXTERNAL_VTK_tiff=ON"
 298                            "-DVTK_MODULE_USE_EXTERNAL_VTK_zlib=ON"
 299                            )
 300        #:phases
 301          (modify-phases %standard-phases
 302            (add-after 'unpack 'patch-sources
 303              (lambda _
 304                (substitute* "Common/Core/vtkFloatingPointExceptions.cxx"
 305                  (("<fenv.h>") "<cfenv>"))
 306                (substitute* "Common/Core/CMakeLists.txt"
 307                  (("fenv.h") "cfenv")))))
 308        #:tests? #f))        ;XXX: test data not included
 309     (inputs
 310      `(("double-conversion" ,double-conversion)
 311        ("eigen" ,eigen)
 312        ("expat" ,expat)
 313        ("freetype" ,freetype)
 314        ("gl2ps" ,gl2ps)
 315        ("glew" ,glew)
 316        ("glu" ,glu)
 317        ("hdf5" ,hdf5)
 318        ("jpeg" ,libjpeg-turbo)
 319        ("jsoncpp" ,jsoncpp)
 320        ("libtheora" ,libtheora)
 321        ("libX11" ,libx11)
 322        ("libxml2" ,libxml2)
 323        ("libXt" ,libxt)
 324        ("lz4" ,lz4)
 325        ("mesa" ,mesa)
 326        ("netcdf" ,netcdf)
 327        ("png" ,libpng)
 328        ("proj" ,proj.4)
 329        ;("pugixml" ,pugixml)
 330        ("sqlite" ,sqlite)
 331        ("tiff" ,libtiff)
 332        ("xorgproto" ,xorgproto)
 333        ("zlib" ,zlib)))
 334     (propagated-inputs
 335      ;; VTK's 'VTK-vtk-module-find-packages.cmake' calls
 336      ;; 'find_package(THEORA)', which in turns looks for libogg.
 337      `(("libogg" ,libogg)))
 338     (home-page "https://vtk.org/")
 339     (synopsis "Libraries for 3D computer graphics")
 340     (description
 341      "The Visualization Toolkit (VTK) is a C++ library for 3D computer graphics,
 342 image processing and visualization.  It supports a wide variety of
 343 visualization algorithms including: scalar, vector, tensor, texture, and
 344 volumetric methods; and advanced modeling techniques such as: implicit
 345 modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay
 346 triangulation.  VTK has an extensive information visualization framework, has
 347 a suite of 3D interaction widgets, supports parallel processing, and
 348 integrates with various databases on GUI toolkits such as Qt and Tk.")
 349     (license license:bsd-3)))
 350
 351 ;; itksnap needs an older variant of VTK.
 352 (define-public vtk-6
 353   (package (inherit vtk)
 354     (version "6.3.0")
 355     (source (origin
 356               (method url-fetch)
 357               (uri (string-append "https://vtk.org/files/release/"
 358                                   (version-major+minor version)
 359                                   "/VTK-" version ".tar.gz"))
 360               (sha256
 361                (base32
 362                 "0pla1r5mvkgl4sl213gfdhzrypdgai0h3z5mfgm6p9jz9hsr794j"))))
 363     (inputs
 364      `(("jsoncpp" ,jsoncpp-for-tensorflow)
 365        ,@(alist-delete "jsoncpp" (package-inputs vtk))))))
 366
 367 (define-public opencv
 368   (package
 369     (name "opencv")
 370     (version "3.4.3")
 371     (source (origin
 372               (method git-fetch)
 373               (uri (git-reference
 374                      (url "https://github.com/opencv/opencv")
 375                      (commit version)))
 376               (file-name (git-file-name name version))
 377               (sha256
 378                (base32
 379                 "06bc61r8myym4s8im10brdjfg4wxkrvsbhhl7vr1msdan2xddzi3"))
 380               (patches
 381                (search-patches "opencv-fix-build-of-grfmt_jpeg2000.cpp.patch"))
 382               (modules '((guix build utils)))
 383               (snippet
 384                '(begin
 385                   ;; Remove external libraries. We have all available in Guix:
 386                   (delete-file-recursively "3rdparty")
 387
 388                   ;; Milky icon set is non-free:
 389                   (delete-file-recursively "modules/highgui/src/files_Qt/Milky")
 390
 391                   ;; Some jars found:
 392                   (for-each delete-file
 393                             '("modules/java/test/pure_test/lib/junit-4.11.jar"
 394                               "samples/java/sbt/sbt/sbt-launch.jar"))
 395                   #t))))
 396     (build-system cmake-build-system)
 397     (arguments
 398      `(#:configure-flags
 399        (list "-DWITH_IPP=OFF"
 400              "-DWITH_ITT=OFF"
 401              "-DWITH_CAROTENE=OFF" ; only visible on arm/aarch64
 402              "-DENABLE_PRECOMPILED_HEADERS=OFF"
 403
 404              ;; CPU-Features:
 405              ;; See cmake/OpenCVCompilerOptimizations.cmake
 406              ;; (CPU_ALL_OPTIMIZATIONS) for a list of all optimizations
 407              ;; BASELINE is the minimum optimization all CPUs must support
 408              ;;
 409              ;; DISPATCH is the list of optional dispatches.
 410              "-DCPU_BASELINE=SSE2"
 411
 412              ,@(match (%current-system)
 413                  ("x86_64-linux"
 414                   '("-DCPU_DISPATCH=NEON;VFPV3;FP16;SSE;SSE2;SSE3;SSSE3;SSE4_1;SSE4_2;POPCNT;AVX;FP16;AVX2;FMA3;AVX_512F;AVX512_SKX"
 415                     "-DCPU_DISPATCH_REQUIRE=SSE3,SSSE3,SSE4_1,SSE4_2,AVX,AVX2"))
 416                  ("armhf-linux"
 417                   '("-DCPU_BASELINE_DISABLE=NEON")) ; causes build failures
 418                  ("aarch64-linux"
 419                   '("-DCPU_BASELINE=NEON"
 420                     "-DCPU_DISPATCH=NEON;VFPV3;FP16"))
 421                  (_ '()))
 422
 423              "-DBUILD_PERF_TESTS=OFF"
 424              "-DBUILD_TESTS=ON"
 425
 426              (string-append "-DOPENCV_EXTRA_MODULES_PATH=" (getcwd)
 427                             "/opencv-contrib/modules")
 428
 429              ;;Define test data:
 430              (string-append "-DOPENCV_TEST_DATA_PATH=" (getcwd)
 431                             "/opencv-extra/testdata")
 432
 433              ;; Is ON by default and would try to rebuild 3rd-party protobuf,
 434              ;; which we had removed, which would lead to an error:
 435              "-DBUILD_PROTOBUF=OFF"
 436
 437              ;; Rebuild protobuf files, because we have a slightly different
 438              ;; version than the included one. If we would not update, we
 439              ;; would get a compile error later:
 440              "-DPROTOBUF_UPDATE_FILES=ON"
 441
 442              ;; xfeatures2d disabled, because it downloads extra binaries from
 443              ;; https://github.com/opencv/opencv_3rdparty
 444              ;; defined in xfeatures2d/cmake/download_{vgg|bootdesc}.cmake
 445              ;; Cmp this bug entry:
 446              ;; https://github.com/opencv/opencv_contrib/issues/1131
 447              "-DBUILD_opencv_xfeatures2d=OFF")
 448        #:phases
 449        (modify-phases %standard-phases
 450          (add-after 'unpack 'disable-broken-tests
 451            (lambda _
 452              ;; These tests fails with:
 453              ;; vtkXOpenGLRenderWindow (0x723990): Could not find a decent config
 454              ;; I think we have no OpenGL support with the Xvfb.
 455              (substitute* '("modules/viz/test/test_tutorial3.cpp"
 456                             "modules/viz/test/test_main.cpp"
 457                             "modules/viz/test/tests_simple.cpp"
 458                             "modules/viz/test/test_viz3d.cpp")
 459                (("(TEST\\(Viz, )([a-z].*\\).*)" all pre post)
 460                 (string-append pre "DISABLED_" post)))
 461
 462              ;; This one fails with "unknown file: Failure"
 463              ;; But I couldn't figure out which file was missing:
 464              (substitute* "../opencv-contrib/modules/face/test/test_face_align.cpp"
 465                (("(TEST\\(CV_Face_FacemarkKazemi, )(can_detect_landmarks\\).*)"
 466                  all pre post)
 467                 (string-append pre "DISABLED_" post)))
 468
 469              ;; Failure reason: Bad accuracy
 470              ;; Incorrect count of accurate poses [2nd case]: 90.000000 / 94.000000
 471              (substitute* "../opencv-contrib/modules/rgbd/test/test_odometry.cpp"
 472                (("(TEST\\(RGBD_Odometry_Rgbd, )(algorithmic\\).*)" all pre post)
 473                 (string-append pre "DISABLED_" post)))
 474              #t))
 475
 476          (add-after 'unpack 'unpack-submodule-sources
 477            (lambda* (#:key inputs #:allow-other-keys)
 478              (mkdir "../opencv-extra")
 479              (mkdir "../opencv-contrib")
 480              (copy-recursively (assoc-ref inputs "opencv-extra")
 481                                "../opencv-extra")
 482              (invoke "tar" "xvf"
 483                      (assoc-ref inputs "opencv-contrib")
 484                      "--strip-components=1"
 485                      "-C" "../opencv-contrib")))
 486
 487          (add-after 'set-paths 'add-ilmbase-include-path
 488            (lambda* (#:key inputs #:allow-other-keys)
 489            ;; OpenEXR propagates ilmbase, but its include files do not appear
 490            ;; in the CPATH, so we need to add "$ilmbase/include/OpenEXR/" to
 491            ;; the CPATH to satisfy the dependency on "ImathVec.h".
 492            (setenv "CPATH"
 493                    (string-append (assoc-ref inputs "ilmbase")
 494                                   "/include/OpenEXR"
 495                                   ":" (or (getenv "CPATH") "")))
 496            #t))
 497        (add-before 'check 'start-xserver
 498          (lambda* (#:key inputs #:allow-other-keys)
 499            (let ((xorg-server (assoc-ref inputs "xorg-server"))
 500                  (disp ":1"))
 501              (setenv "HOME" (getcwd))
 502              (setenv "DISPLAY" disp)
 503              ;; There must be a running X server and make check doesn't start one.
 504              ;; Therefore we must do it.
 505              (zero? (system (format #f "~a/bin/Xvfb ~a &" xorg-server disp)))))))))
 506     (native-inputs
 507      `(("pkg-config" ,pkg-config)
 508        ("xorg-server" ,xorg-server-for-tests) ; For running the tests
 509        ("opencv-extra"
 510         ,(origin
 511            (method git-fetch)
 512            (uri (git-reference
 513                   (url "https://github.com/opencv/opencv_extra")
 514                   (commit version)))
 515            (file-name (git-file-name "opencv_extra" version))
 516            (sha256
 517             (base32 "08p5xnq8n1jw8svvz0fnirfg7q8dm3p4a5dl7527s5xj0f9qn7lp"))))
 518        ("opencv-contrib"
 519         ,(origin
 520            (method git-fetch)
 521            (uri (git-reference
 522                   (url "https://github.com/opencv/opencv_contrib")
 523                   (commit version)))
 524            (file-name (git-file-name "opencv_contrib" version))
 525            (patches (search-patches "opencv-rgbd-aarch64-test-fix.patch"))
 526            (sha256
 527             (base32 "1f334glf39nk42mpqq6j732h3ql2mpz89jd4mcl678s8n73nfjh2"))))))
 528     (inputs `(("libjpeg" ,libjpeg-turbo)
 529               ("libpng" ,libpng)
 530               ("jasper" ,jasper)
 531               ;; ffmpeg 4.0 causes core dumps in tests.
 532               ("ffmpeg" ,ffmpeg-3.4)
 533               ("libtiff" ,libtiff)
 534               ("hdf5" ,hdf5)
 535               ("libgphoto2" ,libgphoto2)
 536               ("libwebp" ,libwebp)
 537               ("zlib" ,zlib)
 538               ("gtkglext" ,gtkglext)
 539               ("openexr" ,openexr)
 540               ("ilmbase" ,ilmbase)
 541               ("gtk+" ,gtk+-2)
 542               ("python-numpy" ,python-numpy)
 543               ("protobuf" ,protobuf)
 544               ("vtk" ,vtk)
 545               ("python" ,python)))
 546     ;; These three CVEs are not a problem of OpenCV, see:
 547     ;; https://github.com/opencv/opencv/issues/10998
 548     (properties '((lint-hidden-cve . ("CVE-2018-7712"
 549                                       "CVE-2018-7713"
 550                                       "CVE-2018-7714"))))
 551     (synopsis "Computer vision library")
 552     (description "OpenCV is a library aimed at
 553 real-time computer vision, including several hundred computer
 554 vision algorithms.  It can be used to do things like:
 555
 556 @itemize
 557 @item image and video input and output
 558 @item image and video processing
 559 @item displaying
 560 @item feature recognition
 561 @item segmentation
 562 @item facial recognition
 563 @item stereo vision
 564 @item structure from motion
 565 @item augmented reality
 566 @item machine learning
 567 @end itemize\n")
 568     (home-page "https://opencv.org/")
 569     (license license:bsd-3)))
 570
 571 (define-public vips
 572   (package
 573     (name "vips")
 574     (version "8.10.6")
 575     (source
 576      (origin
 577        (method url-fetch)
 578        (uri (string-append
 579              "https://github.com/libvips/libvips/releases/download/v"
 580              version "/vips-" version ".tar.gz"))
 581        (sha256
 582         (base32 "0vjsh3i0861f6h9as3bch956cidz824zz499pvhjs3lfjn6hhs14"))))
 583     (build-system gnu-build-system)
 584     (native-inputs
 585      `(("gobject-introspection" ,gobject-introspection)
 586        ("pkg-config" ,pkg-config)))
 587     (inputs
 588      `(("expat" ,expat)
 589        ("fftw" ,fftw)
 590        ("giflib" ,giflib)
 591        ("glib" ,glib)
 592        ("hdf5" ,hdf5)
 593        ("imagemagick" ,imagemagick)
 594        ("lcms" ,lcms)
 595        ("libexif" ,libexif)
 596        ("libgsf" ,libgsf)
 597        ("libjpeg" ,libjpeg-turbo)
 598        ("libpng" ,libpng)
 599        ("librsvg" ,librsvg)
 600        ("libtiff" ,libtiff)
 601        ("libxml2" ,libxml2)
 602        ("libwebp" ,libwebp)
 603        ("matio" ,matio)
 604        ("niftilib" ,niftilib)
 605        ("openexr" ,openexr)
 606        ("orc" ,orc)
 607        ("pango" ,pango)
 608        ("poppler" ,poppler)))
 609     (home-page "https://libvips.github.io/libvips/")
 610     (synopsis "Multithreaded image processing system with low memory needs")
 611     (description
 612      "VIPS is a demand-driven, horizontally threaded image processing library.
 613 It's particularly good at processing large images, working with colour,
 614 scientific analysis, and general research & development.
 615
 616 Compared to most image processing libraries VIPS needs little RAM and runs
 617 quickly, especially on machines with more than one CPU core.  This is primarily
 618 due to its architecture which automatically parallelises the image workflows.")
 619     (license license:lgpl2.1+)))
 620
 621 (define-public gmic
 622   (package
 623     (name "gmic")
 624     (version "2.9.6")
 625     (source
 626      (origin
 627        (method url-fetch)
 628        (uri (string-append "https://gmic.eu/files/source/gmic_"
 629                            version ".tar.gz"))
 630        (sha256
 631         (base32 "06n1dcskky7aqg3a0cp7biwz8agc4xqvr8091l2wsvgib98yhbyj"))))
 632     (build-system cmake-build-system)
 633     (arguments
 634      `(#:tests? #f ;there are no tests
 635        #:configure-flags '("-DBUILD_LIB_STATIC=OFF"
 636                            "-DENABLE_DYNAMIC_LINKING=ON"
 637                            "-DENABLE_LTO=ON")
 638        #:phases
 639        (modify-phases %standard-phases
 640          (add-before 'configure 'set-LDFLAGS
 641            (lambda* (#:key inputs outputs #:allow-other-keys)
 642              (setenv "LDFLAGS"
 643                      (string-append
 644                       "-Wl,-rpath="
 645                       (assoc-ref outputs "out") "/lib")))))))
 646     (native-inputs
 647      `(("pkg-config" ,pkg-config)))
 648     (inputs
 649      `(("curl" ,curl)
 650        ("fftw" ,fftw)
 651        ("graphicsmagick" ,graphicsmagick)
 652        ("libjpeg-turbo" ,libjpeg-turbo)
 653        ("libpng" ,libpng)
 654        ("libtiff" ,libtiff)
 655        ("libx11" ,libx11)
 656        ;;("opencv" ,opencv) ;OpenCV is currently broken in the CI
 657        ("openexr" ,openexr)
 658        ("zlib" ,zlib)))
 659     (home-page "https://gmic.eu/")
 660     (synopsis "Full-featured framework for digital image processing")
 661     (description "G'MIC is a full-featured framework for digital image
 662 processing.  It provides several user interfaces to convert / manipulate
 663 / filter / visualize generic image datasets, ranging from 1D scalar
 664 signals to 3D+t sequences of multi-spectral volumetric images, hence
 665 including 2D color images.")
 666     ;; Dual-licensed, either license applies.
 667     (license (list license:cecill license:cecill-c))))
 668
 669 (define-public gmic-qt
 670   (package
 671     (inherit gmic)
 672     (name "gmic-qt")
 673     (arguments
 674      (substitute-keyword-arguments (package-arguments gmic)
 675        ((#:configure-flags _)
 676         `(list "-DGMIC_QT_HOST=none" "-DENABLE_DYNAMIC_LINKING=ON"
 677                (string-append "-DGMIC_LIB_PATH="
 678                               (assoc-ref %build-inputs "gmic") "/lib")))
 679         ((#:phases phases)
 680          `(modify-phases ,phases
 681             (add-after 'unpack 'qt-chdir
 682               (lambda _ (chdir "gmic-qt") #t))))))
 683     (native-inputs
 684      `(("pkg-config" ,pkg-config)
 685        ("qttools" ,qttools)))
 686     (inputs
 687      `(("gmic" ,gmic)
 688        ("qtbase" ,qtbase)
 689        ,@(package-inputs gmic)))
 690     (synopsis "Qt frontend for the G'MIC image processing framework")
 691     (license license:gpl3+)))
 692
 693 (define-public gmic-qt-krita
 694   (package
 695     (inherit gmic-qt)
 696     (name "gmic-qt-krita")
 697     (arguments
 698      (substitute-keyword-arguments (package-arguments gmic-qt)
 699        ((#:configure-flags flags)
 700         '(list "-DGMIC_QT_HOST=krita" "-DENABLE_DYNAMIC_LINKING=ON"
 701                (string-append "-DGMIC_LIB_PATH="
 702                               (assoc-ref %build-inputs "gmic") "/lib")))))
 703     (synopsis "Krita plugin for the G'MIC image processing framework")))
 704
 705 (define-public nip2
 706   (package
 707     (name "nip2")
 708     (version "8.7.1")
 709     (source
 710      (origin
 711        (method url-fetch)
 712        (uri (string-append "https://github.com/libvips/nip2/releases/download/v"
 713                            version "/nip2-" version ".tar.gz" ))
 714        (sha256
 715         (base32 "0l7n427njif53npqn02gfjjly8y3khbrkzqxp10j5vp9h97psgiw"))))
 716     (build-system gnu-build-system)
 717     (arguments
 718      `(#:phases
 719        (modify-phases %standard-phases
 720          ;; test_conv.ws keep failing so disabling for now.
 721          (add-after 'unpack 'disable-test-conv
 722            (lambda _
 723              (delete-file "test/workspaces/test_conv.ws")
 724              #t))
 725          (add-before 'check 'set-home
 726            (lambda _
 727              (setenv "HOME" "/tmp") #t)))))
 728     (inputs
 729      `(("vips" ,vips)
 730        ("glib" ,glib)
 731        ("libtiff" ,libtiff)
 732        ("gtk+-2" ,gtk+-2)
 733        ("libxml2" ,libxml2)
 734        ("libexif" ,libexif)
 735        ("libjpeg" ,libjpeg-turbo)        ;required by vips.pc
 736        ("librsvg" ,librsvg)
 737        ("fftw" ,fftw)
 738        ("libgsf" ,libgsf)
 739        ("imagemagick" ,imagemagick)
 740        ("orc" ,orc)
 741        ("matio" ,matio)
 742        ("lcms" ,lcms)
 743        ("libwebp" ,libwebp)
 744        ("openexr" ,openexr)
 745        ("poppler" ,poppler)
 746        ("gsl" ,gsl)))
 747     (native-inputs
 748      `(("flex" ,flex)
 749        ("bison" ,bison)
 750        ("pkg-config" ,pkg-config)))
 751     (home-page "https://github.com/libvips/nip2")
 752     (synopsis "Spreadsheet-like GUI for libvips")
 753     (description "This package provide a graphical user interface (GUI) for
 754 the VIPS image processing library.  It's a little like a spreadsheet: you
 755 create a set of formula connecting your objects together, and on a change nip2
 756 recalculates.")
 757     (license license:gpl2+)))
 758
 759 (define-public vxl
 760   (package
 761     (name "vxl")
 762     (version "2.0.2")
 763     (source
 764      (origin
 765        (method git-fetch)
 766        (uri (git-reference
 767              (url "https://github.com/vxl/vxl")
 768              (commit (string-append "v" version))))
 769        (file-name (git-file-name name version))
 770        (sha256
 771         (base32 "0949hw57szq8943f1whwqaz591xjmb19kj803hcv74hdai2b0ycg"))
 772        (modules '((guix build utils)))
 773        ;; TODO: vxl includes an old version of dcmtk.  It won't build with
 774        ;; version 3.6.x.
 775        (snippet
 776         '(begin
 777            (for-each delete-file-recursively
 778                      '("v3p/bzlib/"
 779                        "v3p/geotiff/"
 780                        "v3p/jpeg/"
 781                        "v3p/png/"
 782                        "v3p/tiff/"
 783                        "v3p/zlib/"))
 784            (substitute* "v3p/CMakeLists.txt"
 785              (("add_subdirectory\\((tiff|png|jpeg|zlib|bzlib|geotiff)\\)")
 786               ""))
 787            #t))))
 788     (build-system cmake-build-system)
 789     (inputs
 790      `(("libgeotiff" ,libgeotiff)
 791        ("libtiff" ,libtiff)
 792        ("libjpeg" ,libjpeg-turbo)
 793        ("libpng" ,libpng)
 794        ("zlib" ,zlib)))
 795     (home-page "https://github.com/vxl/vxl/")
 796     (synopsis "Collection of C++ libraries for computer vision")
 797     (description "VXL (the Vision-something-Libraries) is a collection of C++
 798 libraries designed for computer vision research and implementation.")
 799     (license license:bsd-3)))
 800
 801 (define-public vxl-1
 802   (package (inherit vxl)
 803     (name "vxl")
 804     (version "1.18.0")
 805     (source
 806      (origin
 807        (method git-fetch)
 808        (uri (git-reference
 809              (url "https://github.com/vxl/vxl")
 810              (commit (string-append "v" version))))
 811        (file-name (git-file-name name version))
 812        (sha256
 813         (base32 "1g4mr2cc58jwm0vasscbd4y5380wj3ahkvq121z4gs83fhavvxgz"))
 814        (modules '((guix build utils)))
 815        (snippet
 816         '(begin
 817            (for-each delete-file-recursively
 818                      '("v3p/bzlib/"
 819                        "v3p/geotiff/"
 820                        "v3p/png/"
 821                        "v3p/tiff/"
 822                        "v3p/zlib/"))
 823            (substitute* "v3p/CMakeLists.txt"
 824              (("add_subdirectory\\((tiff|png|jpeg|zlib|bzlib|geotiff)\\)")
 825               ""))
 826            #t))))
 827     (arguments
 828      `(#:configure-flags
 829        ;; Needed for itk-snap
 830        (list "-DVNL_CONFIG_LEGACY_METHODS=ON")))))
 831
 832 (define-public insight-toolkit
 833   (package
 834     (name "insight-toolkit")
 835     (version "5.0.0")
 836     (source
 837      (origin
 838        (method url-fetch)
 839        (uri (string-append "https://github.com/InsightSoftwareConsortium/ITK/"
 840                            "releases/download/v" version "/InsightToolkit-"
 841                            version ".tar.xz"))
 842        (sha256
 843         (base32 "0bs63mk4q8jmx38f031jy5w5n9yy5ng9x8ijwinvjyvas8cichqi"))))
 844     (build-system cmake-build-system)
 845     (arguments
 846      `(#:tests? #f            ; tests require network access and external data
 847        #:configure-flags
 848        '("-DITK_USE_GPU=ON"
 849          "-DITK_USE_SYSTEM_LIBRARIES=ON"
 850          "-DITK_USE_SYSTEM_GOOGLETEST=ON"
 851          "-DITK_BUILD_SHARED=ON"
 852          ;; This prevents "GTest::GTest" from being added to the ITK_LIBRARIES
 853          ;; variable in the installed CMake files.  This is necessary as other
 854          ;; packages using insight-toolkit could not be configured otherwise.
 855          "-DGTEST_ROOT=gtest")
 856        #:phases
 857        (modify-phases %standard-phases
 858          (add-after 'unpack 'do-not-tune
 859            (lambda _
 860              (substitute* "CMake/ITKSetStandardCompilerFlags.cmake"
 861                (("-mute=native") ""))
 862              #t)))))
 863     (inputs
 864      `(("eigen" ,eigen)
 865        ("expat" ,expat)
 866        ("fftw" ,fftw)
 867        ("fftwf" ,fftwf)
 868        ("hdf5" ,hdf5)
 869        ("libjpeg" ,libjpeg-turbo)
 870        ("libpng" ,libpng)
 871        ("libtiff" ,libtiff)
 872        ("mesa" ,mesa-opencl)
 873        ("perl" ,perl)
 874        ("python" ,python)
 875        ("tbb" ,tbb)
 876        ("vxl" ,vxl-1)
 877        ("zlib" ,zlib)))
 878     (native-inputs
 879      `(("googletest" ,googletest)
 880        ("pkg-config" ,pkg-config)))
 881     (home-page "https://github.com/InsightSoftwareConsortium/ITK/")
 882     (synopsis "Scientific image processing, segmentation and registration")
 883     (description "The Insight Toolkit (ITK) is a toolkit for N-dimensional
 884 scientific image processing, segmentation, and registration.  Segmentation is
 885 the process of identifying and classifying data found in a digitally sampled
 886 representation.  Typically the sampled representation is an image acquired
 887 from such medical instrumentation as CT or MRI scanners.  Registration is the
 888 task of aligning or developing correspondences between data.  For example, in
 889 the medical environment, a CT scan may be aligned with a MRI scan in order to
 890 combine the information contained in both.")
 891     (license license:asl2.0)))
 892
 893 (define-public insight-toolkit-4
 894   (package (inherit insight-toolkit)
 895     (version "4.13.2")
 896     (source
 897      (origin
 898        (method url-fetch)
 899        (uri (string-append "https://github.com/InsightSoftwareConsortium/ITK/"
 900                            "releases/download/v" version "/InsightToolkit-"
 901                            version ".tar.xz"))
 902        (sha256
 903         (base32 "19cgfpd63gqrvc3m27m394gy2d7w79g5y6lvznb5qqr49lihbgns"))))
 904     (arguments
 905      `(#:tests? #f            ; tests require network access and external data
 906        #:configure-flags
 907        '("-DITKV3_COMPATIBILITY=ON"     ; needed for itk-snap
 908          "-DITK_USE_GPU=ON"
 909          "-DITK_USE_SYSTEM_LIBRARIES=ON"
 910          "-DITK_USE_SYSTEM_GOOGLETEST=ON"
 911          "-DITK_USE_SYSTEM_VXL=ON")))))
 912
 913 (define-public insight-toolkit-4.12
 914   (package (inherit insight-toolkit-4)
 915     (version "4.12.2")
 916     (source
 917      (origin
 918        (method url-fetch)
 919        (uri (string-append "mirror://sourceforge/itk/itk/4.12/"
 920                            "InsightToolkit-" version ".tar.xz"))
 921        (sha256
 922         (base32 "1qw9mxbh083siljygahl4gdfv91xvfd8hfl7ghwii19f60xrvn2w"))))))
 923
 924 (define-public itk-snap
 925   (package
 926     (name "itk-snap")
 927     (version "3.8.0")
 928     (source
 929      (origin
 930        (method git-fetch)
 931        (uri (git-reference
 932              (url "https://git.code.sf.net/p/itk-snap/src")
 933              (commit (string-append "v" version))))
 934        (file-name (git-file-name name version))
 935        (sha256
 936         (base32 "15i5ixpryfrbf3vrrb5rici8fb585f25k0v1ljds16bp1f1msr4q"))))
 937     (build-system cmake-build-system)
 938     (arguments
 939      `(#:configure-flags
 940        (list "-DSNAP_VERSION_GIT_SHA1=release"
 941              "-DSNAP_VERSION_GIT_BRANCH=release"
 942              "-DSNAP_VERSION_GIT_TIMESTAMP=0"
 943              "-DSNAP_PACKAGE_QT_PLUGINS=OFF"
 944              "-DCMAKE_POSITION_INDEPENDENT_CODE=ON")
 945        #:phases
 946        (modify-phases %standard-phases
 947          ;; During the installation phase all libraries provided by all
 948          ;; dependencies will be copied to the lib directory.  That's insane,
 949          ;; so we disable this.
 950          (add-after 'unpack 'do-not-copy-dependencies
 951            (lambda _
 952              (substitute* "CMakeLists.txt"
 953                (("install_qt5_executable\
 954 \\(\\$\\{SNAP_MAIN_INSTALL_DIR\\}/\\$\\{SNAP_EXE\\}\\)")
 955                 ""))
 956              #t))
 957          (add-after 'unpack 'disable-gui-tests
 958            (lambda _
 959              ;; The GUI tests just time out.
 960              (substitute* "CMakeLists.txt"
 961                (("  (Workspace|DiffSpace|ProbeIntensity|RegionCompetition\
 962 |RandomForest|RandomForestBailOut)")
 963                 ""))
 964              #t))
 965          (add-after 'unpack 'make-reproducible
 966            (lambda _
 967              (substitute* "CMakeLists.txt"
 968                (("TODAY\\(SNAP_VERSION_COMPILE_DATE\\)")
 969                 "SET(SNAP_VERSION_COMPILE_DATE \"(removed for reproducibility)\")"))
 970              #t))
 971          (add-after 'unpack 'prepare-submodules
 972            (lambda* (#:key inputs #:allow-other-keys)
 973              (rmdir "Submodules/c3d")
 974              (copy-recursively (assoc-ref inputs "c3d-src")
 975                                "Submodules/c3d")
 976              (substitute* '("Submodules/c3d/adapters/BiasFieldCorrectionN4.cxx"
 977                             "Submodules/c3d/adapters/ApplyMetric.cxx")
 978                (("vcl_") "std::"))
 979              (rmdir "Submodules/greedy")
 980              (symlink (assoc-ref inputs "greedy-src")
 981                       "Submodules/greedy")
 982              #t))
 983          (add-after 'unpack 'fix-includes
 984            (lambda _
 985              (substitute* "GUI/Model/RegistrationModel.cxx"
 986                (("<vnl_symmetric_eigensystem.h>")
 987                 "<vnl/algo/vnl_symmetric_eigensystem.h>"))
 988              #t))
 989          (add-before 'check 'prepare-tests
 990            (lambda _
 991              ;; Needed by at least one test.
 992              (setenv "HOME" "/tmp")
 993              #t))
 994          (add-after 'install 'wrap-executable
 995            (lambda* (#:key inputs outputs #:allow-other-keys)
 996              (let ((out (assoc-ref outputs "out")))
 997                (wrap-program (string-append out "/bin/itksnap")
 998                  `("QT_PLUGIN_PATH" ":" prefix
 999                    ,(map (lambda (label)
1000                            (string-append (assoc-ref inputs label)
1001                                           "/lib/qt5/plugins"))
1002                          '("qtbase" "qtdeclarative"))))
1003                #t))))))
1004     (inputs
1005      `(("curl" ,curl)
1006        ("fftw" ,fftw)
1007        ("fftwf" ,fftwf)
1008        ("glu" ,glu)
1009        ("hdf5" ,hdf5)
1010        ("mesa" ,mesa-opencl)
1011        ;; This package does not build with either insight-toolkit 5.0.0 and
1012        ;; not with 4.13.  It really needs to be 4.12.
1013        ("itk" ,insight-toolkit-4.12)
1014        ("vtk" ,vtk-6)
1015        ("qtbase" ,qtbase)
1016        ("qtdeclarative" ,qtdeclarative)
1017        ("vxl" ,vxl-1)
1018        ("zlib" ,zlib)))
1019     (native-inputs
1020      `(("googletest" ,googletest)
1021        ("qttools" ,qttools)
1022        ("pkg-config" ,pkg-config)
1023        ("c3d-src"
1024         ,(let* ((commit "f521358db26e00002c911cc47bf463b043942ad3")
1025                 (revision "1")
1026                 (version (git-version "0" revision commit)))
1027            (origin
1028              (method git-fetch)
1029              (uri (git-reference
1030                    (url "https://github.com/pyushkevich/c3d")
1031                    (commit commit)))
1032              (file-name (git-file-name "c3d" version))
1033              (sha256
1034               (base32
1035                "0kyv3rxrxwr8c3sa9zv01lsnhk95b27gx1s870k3yi8qp52h7bx3")))))
1036        ;; We are using an arbitrary commit from 2017 because the latest
1037        ;; version breaks the build...
1038        ("greedy-src"
1039         ,(let* ((commit "97e340f7e8e66597599144947775e6039e79a0d3")
1040                 (revision "1")
1041                 (version (git-version "0" revision commit)))
1042            (origin
1043              (method git-fetch)
1044              (uri (git-reference
1045                    (url "https://github.com/pyushkevich/greedy")
1046                    (commit commit)))
1047              (file-name (git-file-name "greedy" version))
1048              (sha256
1049               (base32
1050                "0k5bc9za4jrc8z9dj08z1rkcp5xf0gnd1d2jmi1w9ny4vxh2q2ab")))))))
1051     (home-page "https://sourceforge.net/p/itk-snap/")
1052     (synopsis "Medical image segmentation")
1053     (description "ITK-SNAP is a tool for segmenting anatomical structures in
1054 medical images.  It provides an automatic active contour segmentation
1055 pipeline, along with supporting a manual segmentation toolbox.  ITK-SNAP has a
1056 full-featured UI aimed at clinical researchers.")
1057     ;; This includes the submodules greedy and c3d.
1058     (license license:gpl3+)))
1059
1060 (define-public metapixel
1061   ;; Follow stable branch.
1062   (let ((commit "98ee9daa093b6c334941242e63f90b1c2876eb4f"))
1063     (package
1064       (name "metapixel")
1065       (version (git-version "1.0.2" "1" commit))
1066       (source
1067        (origin
1068          (method git-fetch)
1069          (uri (git-reference
1070                (url "https://github.com/schani/metapixel")
1071                (commit commit)
1072                ;; TODO: Package rwimg and lispreader?
1073                (recursive? #t)))
1074          (file-name (git-file-name name version))
1075          (sha256
1076           (base32 "0r7n3a6bvcxkbpda4mwmrpicii09iql5z69nkjqygkwxw7ny3309"))))
1077       (build-system gnu-build-system)
1078       (inputs
1079        `(("giflib" ,giflib)
1080          ("libjpeg" ,libjpeg-turbo)
1081          ("libpng" ,libpng)
1082          ("perl" ,perl)))
1083       (native-inputs
1084        `(("pkg-config" ,pkg-config)
1085          ("docbook-xml" ,docbook-xml)
1086          ("docbook-xsl" ,docbook-xsl)
1087          ("xsltproc" ,libxslt)))
1088       (arguments
1089        `(#:tests? #f                    ; No tests.
1090          #:make-flags (list
1091                        (string-append "PREFIX=" (assoc-ref %outputs "out"))
1092                        (string-append "MANPAGE_XSL="
1093                                       (assoc-ref %build-inputs "docbook-xsl")
1094                                       "/xml/xsl/docbook-xsl-*/manpages/docbook.xsl"))
1095          #:phases
1096          (modify-phases %standard-phases
1097            (delete 'configure)
1098            (add-before 'install 'make-local-docbook-xml
1099              (lambda* (#:key inputs #:allow-other-keys)
1100                (substitute* "metapixel.xml"
1101                  (("http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd")
1102                   (string-append (assoc-ref inputs "docbook-xml")
1103                                  "/xml/dtd/docbook/docbookx.dtd")))
1104                #t))
1105            (add-before 'install 'fix-directory-creation
1106              (lambda* (#:key outputs #:allow-other-keys)
1107                (mkdir-p (string-append (assoc-ref outputs "out") "/share/man/man1"))
1108                #t)))))
1109       (home-page "https://www.complang.tuwien.ac.at/schani/metapixel/")
1110       (synopsis "Photomosaics generator")
1111       (description "Metapixel is a program for generating photomosaics.  It can
1112 generate classical photomosaics, in which the source image is viewed as a
1113 matrix of equally sized rectangles for each of which a matching image is
1114 substituted, as well as collage-style photomosaics, in which rectangular parts
1115 of the source image at arbitrary positions (i.e. not aligned to a matrix) are
1116 substituted by matching images.")
1117       (license license:gpl2))))
1118
1119 (define-public scantailor-advanced
1120   (let ((commit "3d1e74e6ace413733511086934a66f4e3f7a6027"))
1121     (package
1122       (name "scantailor-advanced")
1123       (version (string-append "1.0.16-" (string-take commit 7)))
1124       (source
1125        (origin
1126          (method git-fetch)
1127          (uri (git-reference
1128                (url "https://github.com/4lex4/scantailor-advanced")
1129                (commit commit)))
1130          (file-name (git-file-name name version))
1131          (sha256
1132           (base32
1133            "0kixwjb2x457dq7927hkh34c803p7yh1pmn6n61rk9shqrcg492h"))))
1134       (build-system qt-build-system)
1135       (native-inputs
1136        `(("qttools" ,qttools)))
1137       (inputs
1138        `(("boost" ,boost)
1139          ("libjpeg" ,libjpeg-turbo)
1140          ("libpng" ,libpng)
1141          ("libtiff" ,libtiff)
1142          ("qtbase" ,qtbase)
1143          ("qtsvg" ,qtsvg)
1144          ("zlib" ,zlib)))
1145       (arguments
1146        `(#:phases
1147          (modify-phases %standard-phases
1148            ;; Some tests require a display and fail with offscreen mode.
1149            (add-after 'unpack 'disable-failing-tests
1150              (lambda _
1151                (setenv "ARGS" "--exclude-regex \"imageproc_.*\"")
1152                #t)))))
1153       (home-page "https://github.com/4lex4/scantailor-advanced")
1154       (synopsis "Clean up scanned pages")
1155       (description "Scan Tailor is an interactive post-processing tool for
1156 scanned pages.  It performs operations such as page splitting, deskewing,
1157 adding/removing borders, and others.  You give it raw scans, and you get pages
1158 ready to be printed or assembled into a PDF or DJVU file.  Scanning, optical
1159 character recognition, and assembling multi-page documents are out of scope of
1160 this project.
1161
1162 Scan Tailer Advanced is a fork of Scan Tailer that merges Scan Tailor Featured
1163 and Scan Tailor Enhanced versions as well as including many more bug fixes.")
1164       (license license:gpl3+))))
1165
1166 (define-public stiff
1167   (package
1168     (name "stiff")
1169     (version "2.4.0")
1170     (source
1171      (origin
1172        (method url-fetch)
1173        (uri (string-append "https://www.astromatic.net/download/stiff/stiff-"
1174                            version ".tar.gz"))
1175        (sha256
1176         (base32 "14m92dskzw7bwsr64ha4p0mj3ndv13gwcbfic3qxrs3zq5353s7l"))))
1177     (build-system gnu-build-system)
1178     (inputs
1179      `(("libtiff" ,libtiff)
1180        ("zlib" ,zlib)
1181        ("libjpeg-turbo" ,libjpeg-turbo)))
1182     (home-page "https://www.astromatic.net/software/stiff")
1183     (synopsis "Convert scientific FITS images to TIFF format")
1184     (description
1185      "STIFF is a program that converts scientific @acronym{FITS, Flexible Image
1186 Transport System} images to the more popular TIFF format for illustration
1187 purposes.")
1188     (license license:gpl3+)))