gnu/packages/image-processing.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2017 John Darrington <jmd@gnu.org>
   3 ;;; Copyright © 2017, 2019 Ricardo Wurmus <rekado@elephly.net>
   4 ;;; Copyright © 2014 Ludovic Courtès <ludo@gnu.org>
   5 ;;; Copyright © 2014 Mark H Weaver <mhw@netris.org>
   6 ;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.org>
   7 ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
   8 ;;; Copyright © 2018 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
   9 ;;; Copyright © 2018 Lprndn <guix@lprndn.info>
  10 ;;; Copyright © 2019 Efraim Flashner <efraim@flashner.co.il>
  11 ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
  12 ;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
  13 ;;; Copyright © 2020 Pierre Neidhardt <mail@ambrevar.xyz>
  14 ;;;
  15 ;;; This file is part of GNU Guix.
  16 ;;;
  17 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  18 ;;; under the terms of the GNU General Public License as published by
  19 ;;; the Free Software Foundation; either version 3 of the License, or (at
  20 ;;; your option) any later version.
  21 ;;;
  22 ;;; GNU Guix is distributed in the hope that it will be useful, but
  23 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  24 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  25 ;;; GNU General Public License for more details.
  26 ;;;
  27 ;;; You should have received a copy of the GNU General Public License
  28 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  29
  30 (define-module (gnu packages image-processing)
  31   #:use-module ((guix licenses) #:prefix license:)
  32   #:use-module (guix packages)
  33   #:use-module (guix utils)
  34   #:use-module (guix download)
  35   #:use-module (guix git-download)
  36   #:use-module (guix build-system cmake)
  37   #:use-module (guix build-system gnu)
  38   #:use-module (gnu packages)
  39   #:use-module (gnu packages algebra)
  40   #:use-module (gnu packages bison)
  41   #:use-module (gnu packages boost)
  42   #:use-module (gnu packages check)
  43   #:use-module (gnu packages compression)
  44   #:use-module (gnu packages curl)
  45   #:use-module (gnu packages docbook)
  46   #:use-module (gnu packages documentation)
  47   #:use-module (gnu packages flex)
  48   #:use-module (gnu packages fontutils)
  49   #:use-module (gnu packages geo)
  50   #:use-module (gnu packages ghostscript)
  51   #:use-module (gnu packages gl)
  52   #:use-module (gnu packages glib)
  53   #:use-module (gnu packages gnome)
  54   #:use-module (gnu packages graphics)
  55   #:use-module (gnu packages graphviz)
  56   #:use-module (gnu packages gstreamer)
  57   #:use-module (gnu packages gtk)
  58   #:use-module (gnu packages image)
  59   #:use-module (gnu packages imagemagick)
  60   #:use-module (gnu packages maths)
  61   #:use-module (gnu packages pdf)
  62   #:use-module (gnu packages perl)
  63   #:use-module (gnu packages photo)
  64   #:use-module (gnu packages pkg-config)
  65   #:use-module (gnu packages protobuf)
  66   #:use-module (gnu packages python)
  67   #:use-module (gnu packages python-xyz)
  68   #:use-module (gnu packages qt)
  69   #:use-module (gnu packages serialization)
  70   #:use-module (gnu packages tbb)
  71   #:use-module (gnu packages tls)
  72   #:use-module (gnu packages video)
  73   #:use-module (gnu packages xiph)
  74   #:use-module (gnu packages xml)
  75   #:use-module (gnu packages xorg)
  76   #:use-module (ice-9 match)
  77   #:use-module (srfi srfi-1))
  78
  79 (define-public dcmtk
  80   (package
  81     (name "dcmtk")
  82     (version "3.6.5")
  83     (source
  84      (origin
  85        (method url-fetch)
  86        (uri
  87         (string-append "ftp://dicom.offis.de/pub/dicom/offis/software/dcmtk/"
  88                        "dcmtk" (string-join (string-split version #\.) "")
  89                        "/dcmtk-" version ".tar.gz"))
  90        (sha256
  91         (base32 "1fdyz5wwjp4grys61mxb2ia9fi6i3ax6s43l16xnv291bxk7hld0"))))
  92     (build-system cmake-build-system)
  93     (inputs
  94      `(;; Our ICU is too recent: “error: ‘UChar’ does not name a type“.
  95        ;; ("icu4c" ,icu4c)
  96        ("libjpeg" ,libjpeg-turbo)
  97        ("libpng" ,libpng)
  98        ("libtiff" ,libtiff)
  99        ("libxml2" ,libxml2)
 100        ("openssl" ,openssl)
 101        ("zlib" ,zlib)))
 102     (native-inputs
 103      `(("doxygen" ,doxygen)))           ; for HTML documentation
 104     (home-page "https://dcmtk.org")
 105     (synopsis "Libraries and programs implementing parts of the DICOM standard")
 106     (description "DCMTK is a collection of libraries and applications
 107 implementing large parts the DICOM standard.  It includes software for
 108 examining, constructing and converting DICOM image files, handling offline
 109 media, sending and receiving images over a network connection, as well as
 110 demonstrative image storage and worklist servers.")
 111     (license (license:fsf-free
 112               "file://COPYRIGHT"
 113               "A union of the Apache 2.0 licence and various non-copyleft
 114 licences similar to the Modified BSD licence."))))
 115
 116 (define-public mia
 117   (package
 118     (name "mia")
 119     (version "2.4.6")
 120     (source (origin
 121               (method url-fetch)
 122               (uri (string-append "mirror://sourceforge/mia/mia/"
 123                                   (version-major+minor version)
 124                                   "/mia-" version ".tar.xz"))
 125               (sha256
 126                (base32
 127                 "0j4nd5z7i3v199jh7hqqhwd4g7snchizkc7rhzanpvngqg91m1pb"))))
 128     (build-system cmake-build-system)
 129     (arguments
 130      `(#:configure-flags
 131        (list "-DMIA_CREATE_NIPYPE_INTERFACES=0"
 132              "-DCMAKE_CXX_FLAGS=-fpermissive")))
 133     (inputs
 134      `(("boost" ,boost)
 135        ("dcmtk" ,dcmtk)
 136        ("doxygen" ,doxygen)
 137        ("eigen" ,eigen)
 138        ("fftw" ,fftw)
 139        ("fftwf" ,fftwf)
 140        ("gsl" ,gsl)
 141        ("gts" ,gts)
 142        ("hdf5" ,hdf5)
 143        ("itpp" ,itpp)
 144        ("libjpeg" ,libjpeg-turbo)
 145        ("libpng" ,libpng)
 146        ("libtiff" ,libtiff)
 147        ("libxml" ,libxml2)
 148        ("libxml++" ,libxml++)
 149        ("maxflow" ,maxflow)
 150        ("niftilib" ,niftilib)
 151        ("nlopt" ,nlopt)
 152        ("openexr" ,openexr)
 153        ("python-lxml" ,python2-lxml)
 154        ("vtk" ,vtk)))
 155     (native-inputs
 156      `(("pkg-config" ,pkg-config)
 157        ("python" ,python-2)))
 158     (home-page "http://mia.sourceforge.net")
 159     (synopsis "Toolkit for gray scale medical image analysis")
 160     (description "MIA provides a combination of command line tools, plug-ins,
 161 and libraries that make it possible run image processing tasks interactively
 162 in a command shell and to prototype using the shell's scripting language.  It
 163 is built around a plug-in structure that makes it easy to add functionality
 164 without compromising the original code base and it makes use of a wide variety
 165 of external libraries that provide additional functionality.")
 166     (license license:gpl3+)))
 167
 168 (define-public vtk
 169   (package
 170     (name "vtk")
 171     (version "8.2.0")
 172     (source (origin
 173               (method url-fetch)
 174               (uri (string-append "https://vtk.org/files/release/"
 175                                   (version-major+minor version)
 176                                   "/VTK-" version ".tar.gz"))
 177               (sha256
 178                (base32
 179                 "1fspgp8k0myr6p2a6wkc21ldcswb4bvmb484m12mxgk1a9vxrhrl"))))
 180     (build-system cmake-build-system)
 181     (arguments
 182      '(#:build-type "Release"           ;Build without '-g' to save space.
 183        ;; -DVTK_USE_SYSTEM_NETCDF:BOOL=TRUE requires netcdf_cxx
 184        #:configure-flags '("-DVTK_USE_SYSTEM_EXPAT:BOOL=TRUE"
 185                            "-DVTK_USE_SYSTEM_FREETYPE:BOOL=TRUE"
 186                            "-DVTK_USE_SYSTEM_HDF5:BOOL=TRUE"
 187                            "-DVTK_USE_SYSTEM_JPEG:BOOL=TRUE"
 188                            "-DVTK_USE_SYSTEM_JSONCPP:BOOL=TRUE"
 189                            "-DVTK_USE_SYSTEM_LIBXML2:BOOL=TRUE"
 190                            "-DVTK_USE_SYSTEM_OGGTHEORA:BOOL=TRUE"
 191                            "-DVTK_USE_SYSTEM_PNG:BOOL=TRUE"
 192                            "-DVTK_USE_SYSTEM_TIFF:BOOL=TRUE"
 193                            "-DVTK_USE_SYSTEM_ZLIB:BOOL=TRUE")
 194        #:tests? #f))                              ;XXX: no "test" target
 195     (inputs
 196      `(("libXt" ,libxt)
 197        ("xorgproto" ,xorgproto)
 198        ("libX11" ,libx11)
 199        ("libxml2" ,libxml2)
 200        ("mesa" ,mesa)
 201        ("glu" ,glu)
 202        ("expat" ,expat)
 203        ("freetype" ,freetype)
 204        ("hdf5" ,hdf5)
 205        ("jpeg" ,libjpeg-turbo)
 206        ("jsoncpp" ,jsoncpp)
 207        ("libogg" ,libogg)
 208        ("libtheora" ,libtheora)
 209        ("png" ,libpng)
 210        ("tiff" ,libtiff)
 211        ("zlib" ,zlib)))
 212     (home-page "https://vtk.org/")
 213     (synopsis "Libraries for 3D computer graphics")
 214     (description
 215      "The Visualization Toolkit (VTK) is a C++ library for 3D computer graphics,
 216 image processing and visualization.  It supports a wide variety of
 217 visualization algorithms including: scalar, vector, tensor, texture, and
 218 volumetric methods; and advanced modeling techniques such as: implicit
 219 modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay
 220 triangulation.  VTK has an extensive information visualization framework, has
 221 a suite of 3D interaction widgets, supports parallel processing, and
 222 integrates with various databases on GUI toolkits such as Qt and Tk.")
 223     (license license:bsd-3)))
 224
 225 ;; itksnap needs an older variant of VTK.
 226 (define-public vtk-6
 227   (package (inherit vtk)
 228     (version "6.3.0")
 229     (source (origin
 230               (method url-fetch)
 231               (uri (string-append "https://vtk.org/files/release/"
 232                                   (version-major+minor version)
 233                                   "/VTK-" version ".tar.gz"))
 234               (sha256
 235                (base32
 236                 "0pla1r5mvkgl4sl213gfdhzrypdgai0h3z5mfgm6p9jz9hsr794j"))))
 237     (inputs
 238      `(("jsoncpp" ,jsoncpp-for-tensorflow)
 239        ,@(alist-delete "jsoncpp" (package-inputs vtk))))))
 240
 241 (define-public opencv
 242   (package
 243     (name "opencv")
 244     (version "3.4.3")
 245     (source (origin
 246               (method git-fetch)
 247               (uri (git-reference
 248                      (url "https://github.com/opencv/opencv")
 249                      (commit version)))
 250               (file-name (git-file-name name version))
 251               (sha256
 252                (base32
 253                 "06bc61r8myym4s8im10brdjfg4wxkrvsbhhl7vr1msdan2xddzi3"))
 254               (modules '((guix build utils)))
 255               (snippet
 256                '(begin
 257                   ;; Remove external libraries. We have all available in Guix:
 258                   (delete-file-recursively "3rdparty")
 259
 260                   ;; Milky icon set is non-free:
 261                   (delete-file-recursively "modules/highgui/src/files_Qt/Milky")
 262
 263                   ;; Some jars found:
 264                   (for-each delete-file
 265                             '("modules/java/test/pure_test/lib/junit-4.11.jar"
 266                               "samples/java/sbt/sbt/sbt-launch.jar"))
 267                   #t))))
 268     (build-system cmake-build-system)
 269     (arguments
 270      `(#:configure-flags
 271        (list "-DWITH_IPP=OFF"
 272              "-DWITH_ITT=OFF"
 273              "-DWITH_CAROTENE=OFF" ; only visible on arm/aarch64
 274              "-DENABLE_PRECOMPILED_HEADERS=OFF"
 275
 276              ;; CPU-Features:
 277              ;; See cmake/OpenCVCompilerOptimizations.cmake
 278              ;; (CPU_ALL_OPTIMIZATIONS) for a list of all optimizations
 279              ;; BASELINE is the minimum optimization all CPUs must support
 280              ;;
 281              ;; DISPATCH is the list of optional dispatches.
 282              "-DCPU_BASELINE=SSE2"
 283
 284              ,@(match (%current-system)
 285                  ("x86_64-linux"
 286                   '("-DCPU_DISPATCH=NEON;VFPV3;FP16;SSE;SSE2;SSE3;SSSE3;SSE4_1;SSE4_2;POPCNT;AVX;FP16;AVX2;FMA3;AVX_512F;AVX512_SKX"
 287                     "-DCPU_DISPATCH_REQUIRE=SSE3,SSSE3,SSE4_1,SSE4_2,AVX,AVX2"))
 288                  ("armhf-linux"
 289                   '("-DCPU_BASELINE_DISABLE=NEON")) ; causes build failures
 290                  ("aarch64-linux"
 291                   '("-DCPU_BASELINE=NEON"
 292                     "-DCPU_DISPATCH=NEON;VFPV3;FP16"))
 293                  (_ '()))
 294
 295              "-DBUILD_PERF_TESTS=OFF"
 296              "-DBUILD_TESTS=ON"
 297
 298              (string-append "-DOPENCV_EXTRA_MODULES_PATH=" (getcwd)
 299                             "/opencv-contrib/modules")
 300
 301              ;;Define test data:
 302              (string-append "-DOPENCV_TEST_DATA_PATH=" (getcwd)
 303                             "/opencv-extra/testdata")
 304
 305              ;; Is ON by default and would try to rebuild 3rd-party protobuf,
 306              ;; which we had removed, which would lead to an error:
 307              "-DBUILD_PROTOBUF=OFF"
 308
 309              ;; Rebuild protobuf files, because we have a slightly different
 310              ;; version than the included one. If we would not update, we
 311              ;; would get a compile error later:
 312              "-DPROTOBUF_UPDATE_FILES=ON"
 313
 314              ;; xfeatures2d disabled, because it downloads extra binaries from
 315              ;; https://github.com/opencv/opencv_3rdparty
 316              ;; defined in xfeatures2d/cmake/download_{vgg|bootdesc}.cmake
 317              ;; Cmp this bug entry:
 318              ;; https://github.com/opencv/opencv_contrib/issues/1131
 319              "-DBUILD_opencv_xfeatures2d=OFF")
 320        #:phases
 321        (modify-phases %standard-phases
 322          (add-after 'unpack 'disable-broken-tests
 323            (lambda _
 324              ;; These tests fails with:
 325              ;; vtkXOpenGLRenderWindow (0x723990): Could not find a decent config
 326              ;; I think we have no OpenGL support with the Xvfb.
 327              (substitute* '("modules/viz/test/test_tutorial3.cpp"
 328                             "modules/viz/test/test_main.cpp"
 329                             "modules/viz/test/tests_simple.cpp"
 330                             "modules/viz/test/test_viz3d.cpp")
 331                (("(TEST\\(Viz, )([a-z].*\\).*)" all pre post)
 332                 (string-append pre "DISABLED_" post)))
 333
 334              ;; This one fails with "unknown file: Failure"
 335              ;; But I couldn't figure out which file was missing:
 336              (substitute* "../opencv-contrib/modules/face/test/test_face_align.cpp"
 337                (("(TEST\\(CV_Face_FacemarkKazemi, )(can_detect_landmarks\\).*)"
 338                  all pre post)
 339                 (string-append pre "DISABLED_" post)))
 340
 341              ;; Failure reason: Bad accuracy
 342              ;; Incorrect count of accurate poses [2nd case]: 90.000000 / 94.000000
 343              (substitute* "../opencv-contrib/modules/rgbd/test/test_odometry.cpp"
 344                (("(TEST\\(RGBD_Odometry_Rgbd, )(algorithmic\\).*)" all pre post)
 345                 (string-append pre "DISABLED_" post)))
 346              #t))
 347
 348          (add-after 'unpack 'unpack-submodule-sources
 349            (lambda* (#:key inputs #:allow-other-keys)
 350              (mkdir "../opencv-extra")
 351              (mkdir "../opencv-contrib")
 352              (copy-recursively (assoc-ref inputs "opencv-extra")
 353                                "../opencv-extra")
 354              (invoke "tar" "xvf"
 355                      (assoc-ref inputs "opencv-contrib")
 356                      "--strip-components=1"
 357                      "-C" "../opencv-contrib")))
 358
 359          (add-after 'set-paths 'add-ilmbase-include-path
 360            (lambda* (#:key inputs #:allow-other-keys)
 361            ;; OpenEXR propagates ilmbase, but its include files do not appear
 362            ;; in the CPATH, so we need to add "$ilmbase/include/OpenEXR/" to
 363            ;; the CPATH to satisfy the dependency on "ImathVec.h".
 364            (setenv "CPATH"
 365                    (string-append (assoc-ref inputs "ilmbase")
 366                                   "/include/OpenEXR"
 367                                   ":" (or (getenv "CPATH") "")))
 368            #t))
 369        (add-before 'check 'start-xserver
 370          (lambda* (#:key inputs #:allow-other-keys)
 371            (let ((xorg-server (assoc-ref inputs "xorg-server"))
 372                  (disp ":1"))
 373              (setenv "HOME" (getcwd))
 374              (setenv "DISPLAY" disp)
 375              ;; There must be a running X server and make check doesn't start one.
 376              ;; Therefore we must do it.
 377              (zero? (system (format #f "~a/bin/Xvfb ~a &" xorg-server disp)))))))))
 378     (native-inputs
 379      `(("pkg-config" ,pkg-config)
 380        ("xorg-server" ,xorg-server-for-tests) ; For running the tests
 381        ("opencv-extra"
 382         ,(origin
 383            (method git-fetch)
 384            (uri (git-reference
 385                   (url "https://github.com/opencv/opencv_extra")
 386                   (commit version)))
 387            (file-name (git-file-name "opencv_extra" version))
 388            (sha256
 389             (base32 "08p5xnq8n1jw8svvz0fnirfg7q8dm3p4a5dl7527s5xj0f9qn7lp"))))
 390        ("opencv-contrib"
 391         ,(origin
 392            (method git-fetch)
 393            (uri (git-reference
 394                   (url "https://github.com/opencv/opencv_contrib")
 395                   (commit version)))
 396            (file-name (git-file-name "opencv_contrib" version))
 397            (patches (search-patches "opencv-rgbd-aarch64-test-fix.patch"))
 398            (sha256
 399             (base32 "1f334glf39nk42mpqq6j732h3ql2mpz89jd4mcl678s8n73nfjh2"))))))
 400     (inputs `(("libjpeg" ,libjpeg-turbo)
 401               ("libpng" ,libpng)
 402               ("jasper" ,jasper)
 403               ;; ffmpeg 4.0 causes core dumps in tests.
 404               ("ffmpeg" ,ffmpeg-3.4)
 405               ("libtiff" ,libtiff)
 406               ("hdf5" ,hdf5)
 407               ("libgphoto2" ,libgphoto2)
 408               ("libwebp" ,libwebp)
 409               ("zlib" ,zlib)
 410               ("gtkglext" ,gtkglext)
 411               ("openexr" ,openexr)
 412               ("ilmbase" ,ilmbase)
 413               ("gtk+" ,gtk+-2)
 414               ("python-numpy" ,python-numpy)
 415               ("protobuf" ,protobuf)
 416               ("vtk" ,vtk)
 417               ("python" ,python)))
 418     ;; These three CVEs are not a problem of OpenCV, see:
 419     ;; https://github.com/opencv/opencv/issues/10998
 420     (properties '((lint-hidden-cve . ("CVE-2018-7712"
 421                                       "CVE-2018-7713"
 422                                       "CVE-2018-7714"))))
 423     (synopsis "Computer vision library")
 424     (description "OpenCV is a library aimed at
 425 real-time computer vision, including several hundred computer
 426 vision algorithms.  It can be used to do things like:
 427
 428 @itemize
 429 @item image and video input and output
 430 @item image and video processing
 431 @item displaying
 432 @item feature recognition
 433 @item segmentation
 434 @item facial recognition
 435 @item stereo vision
 436 @item structure from motion
 437 @item augmented reality
 438 @item machine learning
 439 @end itemize\n")
 440     (home-page "https://opencv.org/")
 441     (license license:bsd-3)))
 442
 443 (define-public vips
 444   (package
 445     (name "vips")
 446     (version "8.7.4")
 447     (source
 448      (origin
 449        (method url-fetch)
 450        (uri (string-append
 451              "https://github.com/libvips/libvips/releases/download/v"
 452              version "/vips-" version ".tar.gz"))
 453        (sha256
 454         (base32 "01gjhcrl6zj7mcj1al717v5jsniahplqhz1xkfh2j78vyfl1hxff"))))
 455     (build-system gnu-build-system)
 456     (native-inputs
 457      `(("pkg-config" ,pkg-config)
 458        ("gobject-introspection" ,gobject-introspection)))
 459     (inputs
 460      `(("glib" ,glib)
 461        ("libjpeg" ,libjpeg-turbo)
 462        ("libpng" ,libpng)
 463        ("librsvg" ,librsvg)
 464        ("libtiff" ,libtiff)
 465        ("libexif" ,libexif)
 466        ("giflib" ,giflib)
 467        ("libgsf" ,libgsf)
 468        ("fftw" ,fftw)
 469        ("poppler" ,poppler)
 470        ("pango" ,pango)
 471        ("lcms" ,lcms)
 472        ("matio" ,matio)
 473        ("libwebp" ,libwebp)
 474        ("niftilib" ,niftilib)
 475        ("openexr" ,openexr)
 476        ("orc" ,orc)
 477        ("imagemagick" ,imagemagick)
 478        ("libxml2" ,libxml2)
 479        ("expat" ,expat)
 480        ("hdf5" ,hdf5)))
 481     (home-page "https://libvips.github.io/libvips/")
 482     (synopsis "Multithreaded image processing system with low memory needs")
 483     (description
 484      "VIPS is a demand-driven, horizontally threaded image processing library.
 485 It's particularly good at processing large images, working with colour,
 486 scientific analysis, and general research & development.
 487
 488 Compared to most image processing libraries VIPS needs little RAM and runs
 489 quickly, especially on machines with more than one CPU core.  This is primarily
 490 due to its architecture which automatically parallelises the image workflows.")
 491     (license license:lgpl2.1+)))
 492
 493 (define-public gmic
 494   (package
 495     (name "gmic")
 496     (version "2.9.1")
 497     (source
 498      (origin
 499        (method url-fetch)
 500        (uri (string-append "https://gmic.eu/files/source/gmic_"
 501                            version ".tar.gz"))
 502        (sha256
 503         (base32 "13axx7nwchn6ysgpvlw3fib474q4nrwv3qn20g3q03ldid0xvjah"))))
 504     (build-system cmake-build-system)
 505     (arguments
 506      `(#:tests? #f))                    ;there are no tests
 507     (native-inputs
 508      `(("pkg-config" ,pkg-config)))
 509     (inputs
 510      `(("curl" ,curl)
 511        ("fftw" ,fftw)
 512        ("graphicsmagick" ,graphicsmagick)
 513        ("libjpeg-turbo" ,libjpeg-turbo)
 514        ("libpng" ,libpng)
 515        ("libtiff" ,libtiff)
 516        ("libx11" ,libx11)
 517        ;;("opencv" ,opencv) ;OpenCV is currently broken in the CI
 518        ("openexr" ,openexr)
 519        ("zlib" ,zlib)))
 520     (home-page "https://gmic.eu/")
 521     (synopsis "Full-featured framework for digital image processing")
 522     (description "G'MIC is a full-featured framework for digital image
 523 processing.  It provides several user interfaces to convert / manipulate
 524 / filter / visualize generic image datasets, ranging from 1D scalar
 525 signals to 3D+t sequences of multi-spectral volumetric images, hence
 526 including 2D color images.")
 527     ;; Dual-licensed, either license applies.
 528     (license (list license:cecill license:cecill-c))))
 529
 530 (define-public nip2
 531   (package
 532     (name "nip2")
 533     (version "8.7.1")
 534     (source
 535      (origin
 536        (method url-fetch)
 537        (uri (string-append "https://github.com/libvips/nip2/releases/download/v"
 538                            version "/nip2-" version ".tar.gz" ))
 539        (sha256
 540         (base32 "0l7n427njif53npqn02gfjjly8y3khbrkzqxp10j5vp9h97psgiw"))))
 541     (build-system gnu-build-system)
 542     (arguments
 543      `(#:phases
 544        (modify-phases %standard-phases
 545          ;; test_conv.ws keep failing so disabling for now.
 546          (add-after 'unpack 'disable-test-conv
 547            (lambda _
 548              (delete-file "test/workspaces/test_conv.ws")
 549              #t))
 550          (add-before 'check 'set-home
 551            (lambda _
 552              (setenv "HOME" "/tmp") #t)))))
 553     (inputs
 554      `(("vips" ,vips)
 555        ("glib" ,glib)
 556        ("libtiff" ,libtiff)
 557        ("gtk+-2" ,gtk+-2)
 558        ("libxml2" ,libxml2)
 559        ("libexif" ,libexif)
 560        ("libjpeg" ,libjpeg-turbo)        ;required by vips.pc
 561        ("librsvg" ,librsvg)
 562        ("fftw" ,fftw)
 563        ("libgsf" ,libgsf)
 564        ("imagemagick" ,imagemagick)
 565        ("orc" ,orc)
 566        ("matio" ,matio)
 567        ("lcms" ,lcms)
 568        ("libwebp" ,libwebp)
 569        ("openexr" ,openexr)
 570        ("poppler" ,poppler)
 571        ("gsl" ,gsl)))
 572     (native-inputs
 573      `(("flex" ,flex)
 574        ("bison" ,bison)
 575        ("pkg-config" ,pkg-config)))
 576     (home-page "https://github.com/libvips/nip2")
 577     (synopsis "Spreadsheet-like GUI for libvips")
 578     (description "This package provide a graphical user interface (GUI) for
 579 the VIPS image processing library.  It's a little like a spreadsheet: you
 580 create a set of formula connecting your objects together, and on a change nip2
 581 recalculates.")
 582     (license license:gpl2+)))
 583
 584 (define-public vxl
 585   (package
 586     (name "vxl")
 587     (version "2.0.2")
 588     (source
 589      (origin
 590        (method git-fetch)
 591        (uri (git-reference
 592              (url "https://github.com/vxl/vxl")
 593              (commit (string-append "v" version))))
 594        (file-name (git-file-name name version))
 595        (sha256
 596         (base32 "0949hw57szq8943f1whwqaz591xjmb19kj803hcv74hdai2b0ycg"))
 597        (modules '((guix build utils)))
 598        ;; TODO: vxl includes an old version of dcmtk.  It won't build with
 599        ;; version 3.6.x.
 600        (snippet
 601         '(begin
 602            (for-each delete-file-recursively
 603                      '("v3p/bzlib/"
 604                        "v3p/geotiff/"
 605                        "v3p/jpeg/"
 606                        "v3p/png/"
 607                        "v3p/tiff/"
 608                        "v3p/zlib/"))
 609            (substitute* "v3p/CMakeLists.txt"
 610              (("add_subdirectory\\((tiff|png|jpeg|zlib|bzlib|geotiff)\\)")
 611               ""))
 612            #t))))
 613     (build-system cmake-build-system)
 614     (inputs
 615      `(("libgeotiff" ,libgeotiff)
 616        ("libtiff" ,libtiff)
 617        ("libjpeg" ,libjpeg-turbo)
 618        ("libpng" ,libpng)
 619        ("zlib" ,zlib)))
 620     (home-page "https://github.com/vxl/vxl/")
 621     (synopsis "Collection of C++ libraries for computer vision")
 622     (description "VXL (the Vision-something-Libraries) is a collection of C++
 623 libraries designed for computer vision research and implementation.")
 624     (license license:bsd-3)))
 625
 626 (define-public vxl-1
 627   (package (inherit vxl)
 628     (name "vxl")
 629     (version "1.18.0")
 630     (source
 631      (origin
 632        (method git-fetch)
 633        (uri (git-reference
 634              (url "https://github.com/vxl/vxl")
 635              (commit (string-append "v" version))))
 636        (file-name (git-file-name name version))
 637        (sha256
 638         (base32 "1g4mr2cc58jwm0vasscbd4y5380wj3ahkvq121z4gs83fhavvxgz"))
 639        (modules '((guix build utils)))
 640        (snippet
 641         '(begin
 642            (for-each delete-file-recursively
 643                      '("v3p/bzlib/"
 644                        "v3p/geotiff/"
 645                        "v3p/png/"
 646                        "v3p/tiff/"
 647                        "v3p/zlib/"))
 648            (substitute* "v3p/CMakeLists.txt"
 649              (("add_subdirectory\\((tiff|png|jpeg|zlib|bzlib|geotiff)\\)")
 650               ""))
 651            #t))))
 652     (arguments
 653      `(#:configure-flags
 654        ;; Needed for itk-snap
 655        (list "-DVNL_CONFIG_LEGACY_METHODS=ON")))))
 656
 657 (define-public insight-toolkit
 658   (package
 659     (name "insight-toolkit")
 660     (version "5.0.0")
 661     (source
 662      (origin
 663        (method url-fetch)
 664        (uri (string-append "https://github.com/InsightSoftwareConsortium/ITK/"
 665                            "releases/download/v" version "/InsightToolkit-"
 666                            version ".tar.xz"))
 667        (sha256
 668         (base32 "0bs63mk4q8jmx38f031jy5w5n9yy5ng9x8ijwinvjyvas8cichqi"))))
 669     (build-system cmake-build-system)
 670     (arguments
 671      `(#:tests? #f            ; tests require network access and external data
 672        #:configure-flags
 673        '("-DITK_USE_GPU=ON"
 674          "-DITK_USE_SYSTEM_LIBRARIES=ON"
 675          "-DITK_USE_SYSTEM_GOOGLETEST=ON"
 676          "-DITK_BUILD_SHARED=ON"
 677          ;; This prevents "GTest::GTest" from being added to the ITK_LIBRARIES
 678          ;; variable in the installed CMake files.  This is necessary as other
 679          ;; packages using insight-toolkit could not be configured otherwise.
 680          "-DGTEST_ROOT=gtest")
 681        #:phases
 682        (modify-phases %standard-phases
 683          (add-after 'unpack 'do-not-tune
 684            (lambda _
 685              (substitute* "CMake/ITKSetStandardCompilerFlags.cmake"
 686                (("-mute=native") ""))
 687              #t)))))
 688     (inputs
 689      `(("eigen" ,eigen)
 690        ("expat" ,expat)
 691        ("fftw" ,fftw)
 692        ("fftwf" ,fftwf)
 693        ("hdf5" ,hdf5)
 694        ("libjpeg" ,libjpeg-turbo)
 695        ("libpng" ,libpng)
 696        ("libtiff" ,libtiff)
 697        ("mesa" ,mesa-opencl)
 698        ("perl" ,perl)
 699        ("python" ,python)
 700        ("tbb" ,tbb)
 701        ("vxl" ,vxl-1)
 702        ("zlib" ,zlib)))
 703     (native-inputs
 704      `(("googletest" ,googletest)
 705        ("pkg-config" ,pkg-config)))
 706     (home-page "https://github.com/InsightSoftwareConsortium/ITK/")
 707     (synopsis "Scientific image processing, segmentation and registration")
 708     (description "The Insight Toolkit (ITK) is a toolkit for N-dimensional
 709 scientific image processing, segmentation, and registration.  Segmentation is
 710 the process of identifying and classifying data found in a digitally sampled
 711 representation.  Typically the sampled representation is an image acquired
 712 from such medical instrumentation as CT or MRI scanners.  Registration is the
 713 task of aligning or developing correspondences between data.  For example, in
 714 the medical environment, a CT scan may be aligned with a MRI scan in order to
 715 combine the information contained in both.")
 716     (license license:asl2.0)))
 717
 718 (define-public insight-toolkit-4
 719   (package (inherit insight-toolkit)
 720     (version "4.13.2")
 721     (source
 722      (origin
 723        (method url-fetch)
 724        (uri (string-append "https://github.com/InsightSoftwareConsortium/ITK/"
 725                            "releases/download/v" version "/InsightToolkit-"
 726                            version ".tar.xz"))
 727        (sha256
 728         (base32 "19cgfpd63gqrvc3m27m394gy2d7w79g5y6lvznb5qqr49lihbgns"))))
 729     (arguments
 730      `(#:tests? #f            ; tests require network access and external data
 731        #:configure-flags
 732        '("-DITKV3_COMPATIBILITY=ON"     ; needed for itk-snap
 733          "-DITK_USE_GPU=ON"
 734          "-DITK_USE_SYSTEM_LIBRARIES=ON"
 735          "-DITK_USE_SYSTEM_GOOGLETEST=ON"
 736          "-DITK_USE_SYSTEM_VXL=ON")))))
 737
 738 (define-public insight-toolkit-4.12
 739   (package (inherit insight-toolkit-4)
 740     (version "4.12.2")
 741     (source
 742      (origin
 743        (method url-fetch)
 744        (uri (string-append "mirror://sourceforge/itk/itk/4.12/"
 745                            "InsightToolkit-" version ".tar.xz"))
 746        (sha256
 747         (base32 "1qw9mxbh083siljygahl4gdfv91xvfd8hfl7ghwii19f60xrvn2w"))))))
 748
 749 (define-public itk-snap
 750   (package
 751     (name "itk-snap")
 752     (version "3.8.0")
 753     (source
 754      (origin
 755        (method git-fetch)
 756        (uri (git-reference
 757              (url "https://git.code.sf.net/p/itk-snap/src")
 758              (commit (string-append "v" version))))
 759        (file-name (git-file-name name version))
 760        (sha256
 761         (base32 "15i5ixpryfrbf3vrrb5rici8fb585f25k0v1ljds16bp1f1msr4q"))))
 762     (build-system cmake-build-system)
 763     (arguments
 764      `(#:configure-flags
 765        (list "-DSNAP_VERSION_GIT_SHA1=release"
 766              "-DSNAP_VERSION_GIT_BRANCH=release"
 767              "-DSNAP_VERSION_GIT_TIMESTAMP=0"
 768              "-DSNAP_PACKAGE_QT_PLUGINS=OFF"
 769              "-DCMAKE_POSITION_INDEPENDENT_CODE=ON")
 770        #:phases
 771        (modify-phases %standard-phases
 772          ;; During the installation phase all libraries provided by all
 773          ;; dependencies will be copied to the lib directory.  That's insane,
 774          ;; so we disable this.
 775          (add-after 'unpack 'do-not-copy-dependencies
 776            (lambda _
 777              (substitute* "CMakeLists.txt"
 778                (("install_qt5_executable\
 779 \\(\\$\\{SNAP_MAIN_INSTALL_DIR\\}/\\$\\{SNAP_EXE\\}\\)")
 780                 ""))
 781              #t))
 782          (add-after 'unpack 'disable-gui-tests
 783            (lambda _
 784              ;; The GUI tests just time out.
 785              (substitute* "CMakeLists.txt"
 786                (("  (Workspace|DiffSpace|ProbeIntensity|RegionCompetition\
 787 |RandomForest|RandomForestBailOut)")
 788                 ""))
 789              #t))
 790          (add-after 'unpack 'make-reproducible
 791            (lambda _
 792              (substitute* "CMakeLists.txt"
 793                (("TODAY\\(SNAP_VERSION_COMPILE_DATE\\)")
 794                 "SET(SNAP_VERSION_COMPILE_DATE \"(removed for reproducibility)\")"))
 795              #t))
 796          (add-after 'unpack 'prepare-submodules
 797            (lambda* (#:key inputs #:allow-other-keys)
 798              (rmdir "Submodules/c3d")
 799              (copy-recursively (assoc-ref inputs "c3d-src")
 800                                "Submodules/c3d")
 801              (substitute* '("Submodules/c3d/adapters/BiasFieldCorrectionN4.cxx"
 802                             "Submodules/c3d/adapters/ApplyMetric.cxx")
 803                (("vcl_") "std::"))
 804              (rmdir "Submodules/greedy")
 805              (symlink (assoc-ref inputs "greedy-src")
 806                       "Submodules/greedy")
 807              #t))
 808          (add-after 'unpack 'fix-includes
 809            (lambda _
 810              (substitute* "GUI/Model/RegistrationModel.cxx"
 811                (("<vnl_symmetric_eigensystem.h>")
 812                 "<vnl/algo/vnl_symmetric_eigensystem.h>"))
 813              #t))
 814          (add-before 'check 'prepare-tests
 815            (lambda _
 816              ;; Needed by at least one test.
 817              (setenv "HOME" "/tmp")
 818              #t))
 819          (add-after 'install 'wrap-executable
 820            (lambda* (#:key inputs outputs #:allow-other-keys)
 821              (let ((out (assoc-ref outputs "out")))
 822                (wrap-program (string-append out "/bin/itksnap")
 823                  `("QT_PLUGIN_PATH" ":" prefix
 824                    ,(map (lambda (label)
 825                            (string-append (assoc-ref inputs label)
 826                                           "/lib/qt5/plugins"))
 827                          '("qtbase" "qtdeclarative"))))
 828                #t))))))
 829     (inputs
 830      `(("curl" ,curl)
 831        ("fftw" ,fftw)
 832        ("fftwf" ,fftwf)
 833        ("glu" ,glu)
 834        ("hdf5" ,hdf5)
 835        ("mesa" ,mesa-opencl)
 836        ;; This package does not build with either insight-toolkit 5.0.0 and
 837        ;; not with 4.13.  It really needs to be 4.12.
 838        ("itk" ,insight-toolkit-4.12)
 839        ("vtk" ,vtk-6)
 840        ("qtbase" ,qtbase)
 841        ("qtdeclarative" ,qtdeclarative)
 842        ("vxl" ,vxl-1)
 843        ("zlib" ,zlib)))
 844     (native-inputs
 845      `(("googletest" ,googletest)
 846        ("qttools" ,qttools)
 847        ("pkg-config" ,pkg-config)
 848        ("c3d-src"
 849         ,(let* ((commit "f521358db26e00002c911cc47bf463b043942ad3")
 850                 (revision "1")
 851                 (version (git-version "0" revision commit)))
 852            (origin
 853              (method git-fetch)
 854              (uri (git-reference
 855                    (url "https://github.com/pyushkevich/c3d")
 856                    (commit commit)))
 857              (file-name (git-file-name "c3d" version))
 858              (sha256
 859               (base32
 860                "0kyv3rxrxwr8c3sa9zv01lsnhk95b27gx1s870k3yi8qp52h7bx3")))))
 861        ;; We are using an arbitrary commit from 2017 because the latest
 862        ;; version breaks the build...
 863        ("greedy-src"
 864         ,(let* ((commit "97e340f7e8e66597599144947775e6039e79a0d3")
 865                 (revision "1")
 866                 (version (git-version "0" revision commit)))
 867            (origin
 868              (method git-fetch)
 869              (uri (git-reference
 870                    (url "https://github.com/pyushkevich/greedy")
 871                    (commit commit)))
 872              (file-name (git-file-name "greedy" version))
 873              (sha256
 874               (base32
 875                "0k5bc9za4jrc8z9dj08z1rkcp5xf0gnd1d2jmi1w9ny4vxh2q2ab")))))))
 876     (home-page "https://sourceforge.net/p/itk-snap/")
 877     (synopsis "Medical image segmentation")
 878     (description "ITK-SNAP is a tool for segmenting anatomical structures in
 879 medical images.  It provides an automatic active contour segmentation
 880 pipeline, along with supporting a manual segmentation toolbox.  ITK-SNAP has a
 881 full-featured UI aimed at clinical researchers.")
 882     ;; This includes the submodules greedy and c3d.
 883     (license license:gpl3+)))
 884
 885 (define-public metapixel
 886   ;; Follow stable branch.
 887   (let ((commit "98ee9daa093b6c334941242e63f90b1c2876eb4f"))
 888     (package
 889       (name "metapixel")
 890       (version (git-version "1.0.2" "1" commit))
 891       (source
 892        (origin
 893          (method git-fetch)
 894          (uri (git-reference
 895                (url "https://github.com/schani/metapixel")
 896                (commit commit)
 897                ;; TODO: Package rwimg and lispreader?
 898                (recursive? #t)))
 899          (file-name (git-file-name name version))
 900          (sha256
 901           (base32 "0r7n3a6bvcxkbpda4mwmrpicii09iql5z69nkjqygkwxw7ny3309"))))
 902       (build-system gnu-build-system)
 903       (inputs
 904        `(("giflib" ,giflib)
 905          ("libjpeg" ,libjpeg-turbo)
 906          ("libpng" ,libpng)
 907          ("perl" ,perl)))
 908       (native-inputs
 909        `(("pkg-config" ,pkg-config)
 910          ("docbook-xml" ,docbook-xml)
 911          ("docbook-xsl" ,docbook-xsl)
 912          ("xsltproc" ,libxslt)))
 913       (arguments
 914        `(#:tests? #f                    ; No tests.
 915          #:make-flags (list
 916                        (string-append "PREFIX=" (assoc-ref %outputs "out"))
 917                        (string-append "MANPAGE_XSL="
 918                                       (assoc-ref %build-inputs "docbook-xsl")
 919                                       "/xml/xsl/docbook-xsl-*/manpages/docbook.xsl"))
 920          #:phases
 921          (modify-phases %standard-phases
 922            (delete 'configure)
 923            (add-before 'install 'make-local-docbook-xml
 924              (lambda* (#:key inputs #:allow-other-keys)
 925                (substitute* "metapixel.xml"
 926                  (("http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd")
 927                   (string-append (assoc-ref inputs "docbook-xml")
 928                                  "/xml/dtd/docbook/docbookx.dtd")))
 929                #t))
 930            (add-before 'install 'fix-directory-creation
 931              (lambda* (#:key outputs #:allow-other-keys)
 932                (mkdir-p (string-append (assoc-ref outputs "out") "/share/man/man1"))
 933                #t)))))
 934       (home-page "https://www.complang.tuwien.ac.at/schani/metapixel/")
 935       (synopsis "Photomosaics generator")
 936       (description "Metapixel is a program for generating photomosaics.  It can
 937 generate classical photomosaics, in which the source image is viewed as a
 938 matrix of equally sized rectangles for each of which a matching image is
 939 substitued, as well as collage-style photomosaics, in which rectangular parts
 940 of the source image at arbitrary positions (i.e. not aligned to a matrix) are
 941 substituted by matching images.")
 942       (license license:gpl2))))