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