gnu/packages/image-processing.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2017 John Darrington <jmd@gnu.org>
   3 ;;; Copyright © 2017 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 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 ;;;
  12 ;;; This file is part of GNU Guix.
  13 ;;;
  14 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  15 ;;; under the terms of the GNU General Public License as published by
  16 ;;; the Free Software Foundation; either version 3 of the License, or (at
  17 ;;; your option) any later version.
  18 ;;;
  19 ;;; GNU Guix is distributed in the hope that it will be useful, but
  20 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  21 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  22 ;;; GNU General Public License for more details.
  23 ;;;
  24 ;;; You should have received a copy of the GNU General Public License
  25 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  26
  27 (define-module (gnu packages image-processing)
  28   #:use-module ((guix licenses) #:prefix license:)
  29   #:use-module (guix packages)
  30   #:use-module (guix utils)
  31   #:use-module (guix download)
  32   #:use-module (guix build-system cmake)
  33   #:use-module (guix build-system gnu)
  34   #:use-module (gnu packages)
  35   #:use-module (gnu packages algebra)
  36   #:use-module (gnu packages bison)
  37   #:use-module (gnu packages boost)
  38   #:use-module (gnu packages compression)
  39   #:use-module (gnu packages documentation)
  40   #:use-module (gnu packages flex)
  41   #:use-module (gnu packages fontutils)
  42   #:use-module (gnu packages ghostscript)
  43   #:use-module (gnu packages gl)
  44   #:use-module (gnu packages glib)
  45   #:use-module (gnu packages gnome)
  46   #:use-module (gnu packages graphics)
  47   #:use-module (gnu packages graphviz)
  48   #:use-module (gnu packages gstreamer)
  49   #:use-module (gnu packages gtk)
  50   #:use-module (gnu packages image)
  51   #:use-module (gnu packages imagemagick)
  52   #:use-module (gnu packages maths)
  53   #:use-module (gnu packages pdf)
  54   #:use-module (gnu packages perl)
  55   #:use-module (gnu packages photo)
  56   #:use-module (gnu packages pkg-config)
  57   #:use-module (gnu packages protobuf)
  58   #:use-module (gnu packages python)
  59   #:use-module (gnu packages serialization)
  60   #:use-module (gnu packages video)
  61   #:use-module (gnu packages xiph)
  62   #:use-module (gnu packages xml)
  63   #:use-module (gnu packages xorg))
  64
  65 ;; We use the latest snapshot of this package because the latest release is
  66 ;; from 2011 and has known vulnerabilities that cannot easily be fixed by
  67 ;; applying patches.
  68 (define-public dcmtk
  69   (package
  70     (name "dcmtk")
  71     (version "3.6.1_20170228")
  72     (source (origin
  73               (method url-fetch)
  74               (uri (string-append "ftp://dicom.offis.de/pub/dicom/offis/"
  75                                   "software/dcmtk/snapshot/dcmtk-"
  76                                   version ".tar.gz"))
  77               (sha256
  78                (base32
  79                 "04cwfx8yrscqcd59mxk2fh6314ckayi9cp68iql5a57pf2pg5qld"))))
  80     (build-system gnu-build-system)
  81     (inputs
  82      `(("libtiff" ,libtiff)
  83        ("libpng" ,libpng)
  84        ("doxygen" ,doxygen)
  85        ("zlib" ,zlib)))
  86     (native-inputs
  87      `(("perl" ,perl)))
  88     (home-page "http://dcmtk.org")
  89     (synopsis "Libraries and programs implementing parts of the DICOM standard")
  90     (description "DCMTK is a collection of libraries and applications
  91 implementing large parts the DICOM standard.  It includes software for
  92 examining, constructing and converting DICOM image files, handling offline
  93 media, sending and receiving images over a network connection, as well as
  94 demonstrative image storage and worklist servers.")
  95     (license (license:fsf-free
  96               "file://COPYRIGHT"
  97               "A union of the Apache 2.0 licence and various non-copyleft
  98 licences similar to the Modified BSD licence."))))
  99
 100 (define-public mia
 101   (package
 102     (name "mia")
 103     (version "2.4.6")
 104     (source (origin
 105               (method url-fetch)
 106               (uri (string-append "mirror://sourceforge/mia/mia/"
 107                                   (version-major+minor version)
 108                                   "/mia-" version ".tar.xz"))
 109               (sha256
 110                (base32
 111                 "0j4nd5z7i3v199jh7hqqhwd4g7snchizkc7rhzanpvngqg91m1pb"))))
 112     (build-system cmake-build-system)
 113     (arguments
 114      `(#:configure-flags
 115        (list "-DMIA_CREATE_NIPYPE_INTERFACES=0"
 116              "-DCMAKE_CXX_FLAGS=-fpermissive")))
 117     (inputs
 118      `(("boost" ,boost)
 119        ("dcmtk" ,dcmtk)
 120        ("doxygen" ,doxygen)
 121        ("eigen" ,eigen)
 122        ("fftw" ,fftw)
 123        ("fftwf" ,fftwf)
 124        ("gsl" ,gsl)
 125        ("gts" ,gts)
 126        ("hdf5" ,hdf5)
 127        ("itpp" ,itpp)
 128        ("libjpeg" ,libjpeg)
 129        ("libpng" ,libpng)
 130        ("libtiff" ,libtiff)
 131        ("libxml" ,libxml2)
 132        ("libxml++" ,libxml++)
 133        ("maxflow" ,maxflow)
 134        ("niftilib" ,niftilib)
 135        ("nlopt" ,nlopt)
 136        ("openexr" ,openexr)
 137        ("python-lxml" ,python2-lxml)
 138        ("vtk" ,vtk)))
 139     (native-inputs
 140      `(("pkg-config" ,pkg-config)
 141        ("python" ,python-2)))
 142     (home-page "http://mia.sourceforge.net")
 143     (synopsis "Toolkit for gray scale medical image analysis")
 144     (description "MIA provides a combination of command line tools, plug-ins,
 145 and libraries that make it possible run image processing tasks interactively
 146 in a command shell and to prototype using the shell's scripting language.  It
 147 is built around a plug-in structure that makes it easy to add functionality
 148 without compromising the original code base and it makes use of a wide variety
 149 of external libraries that provide additional functionality.")
 150     (license license:gpl3+)))
 151
 152 (define-public vtk
 153   (package
 154     (name "vtk")
 155     (version "7.1.0")
 156     (source (origin
 157               (method url-fetch)
 158               (uri (string-append "http://www.vtk.org/files/release/"
 159                                   (version-major+minor version)
 160                                   "/VTK-" version ".tar.gz"))
 161               (sha256
 162                (base32
 163                 "0yj96z58haan77gzilnqp7xpf8hg5jk11a3jx55p2ksd400s0gjz"))))
 164     (build-system cmake-build-system)
 165     (arguments
 166      '(#:build-type "Release"           ;Build without '-g' to save space.
 167        ;; -DVTK_USE_SYSTEM_NETCDF:BOOL=TRUE requires netcdf_cxx
 168        #:configure-flags '("-DVTK_USE_SYSTEM_EXPAT:BOOL=TRUE"
 169                            "-DVTK_USE_SYSTEM_FREETYPE:BOOL=TRUE"
 170                            "-DVTK_USE_SYSTEM_HDF5:BOOL=TRUE"
 171                            "-DVTK_USE_SYSTEM_JPEG:BOOL=TRUE"
 172                            "-DVTK_USE_SYSTEM_JSONCPP:BOOL=TRUE"
 173                            "-DVTK_USE_SYSTEM_LIBXML2:BOOL=TRUE"
 174                            "-DVTK_USE_SYSTEM_OGGTHEORA:BOOL=TRUE"
 175                            "-DVTK_USE_SYSTEM_PNG:BOOL=TRUE"
 176                            "-DVTK_USE_SYSTEM_TIFF:BOOL=TRUE"
 177                            "-DVTK_USE_SYSTEM_ZLIB:BOOL=TRUE")
 178        #:tests? #f))                              ;XXX: no "test" target
 179     (inputs
 180      `(("libXt" ,libxt)
 181        ("xorgproto" ,xorgproto)
 182        ("libX11" ,libx11)
 183        ("libxml2" ,libxml2)
 184        ("mesa" ,mesa)
 185        ("glu" ,glu)
 186        ("expat" ,expat)
 187        ("freetype" ,freetype)
 188        ("hdf5" ,hdf5)
 189        ("jpeg" ,libjpeg)
 190        ("jsoncpp" ,jsoncpp)
 191        ("libogg" ,libogg)
 192        ("libtheora" ,libtheora)
 193        ("png" ,libpng)
 194        ("tiff" ,libtiff)
 195        ("zlib" ,zlib)))
 196     (home-page "http://www.vtk.org/")
 197     (synopsis "Libraries for 3D computer graphics")
 198     (description
 199      "The Visualization Toolkit (VTK) is a C++ library for 3D computer graphics,
 200 image processing and visualization.  It supports a wide variety of
 201 visualization algorithms including: scalar, vector, tensor, texture, and
 202 volumetric methods; and advanced modeling techniques such as: implicit
 203 modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay
 204 triangulation.  VTK has an extensive information visualization framework, has
 205 a suite of 3D interaction widgets, supports parallel processing, and
 206 integrates with various databases on GUI toolkits such as Qt and Tk.")
 207     (license license:bsd-3)))
 208
 209 (define-public opencv
 210   (package
 211     (name "opencv")
 212     (version "3.4.3")
 213     (source (origin
 214               (method url-fetch)
 215               (uri (string-append "https://github.com/opencv/opencv/archive/"
 216                                   version ".zip"))
 217               (file-name (string-append name "-" version ".zip"))
 218               (sha256
 219                (base32
 220                 "0pycx1pz8lj794q32mlalyc3ijqxwsyin65r26nh4yc0p71xiirp"))
 221               (modules '((guix build utils)))
 222               (snippet
 223                '(begin
 224                   ;; Remove external libraries. We have all available in Guix:
 225                   (delete-file-recursively "3rdparty")
 226
 227                   ;; Milky icon set is non-free:
 228                   (delete-file-recursively "modules/highgui/src/files_Qt/Milky")
 229
 230                   ;; Some jars found:
 231                   (for-each delete-file
 232                             '("modules/java/test/pure_test/lib/junit-4.11.jar"
 233                               "samples/java/sbt/sbt/sbt-launch.jar"))))))
 234     (build-system cmake-build-system)
 235     (arguments
 236      `(#:configure-flags
 237        (list "-DWITH_IPP=OFF"
 238              "-DWITH_ITT=OFF"
 239              "-DWITH_CAROTENE=OFF" ; only visible on arm/aarch64
 240              "-DENABLE_PRECOMPILED_HEADERS=OFF"
 241
 242              ;; CPU-Features:
 243              ;; See cmake/OpenCVCompilerOptimizations.cmake
 244              ;; (CPU_ALL_OPTIMIZATIONS) for a list of all optimizations
 245              ;; BASELINE is the minimum optimization all CPUs must support
 246              ;;
 247              ;; DISPATCH is the list of optional dispatches. We add them all.
 248              "-DCPU_BASELINE=SSE2, NEON"
 249
 250              "-DCPU_DISPATCH=NEON;VFPV3;FP16;SSE;SSE2;SSE3;SSSE3;SSE4_1;SSE4_2;POPCNT;AVX;FP16;AVX2;FMA3;AVX_512F;AVX512_SKX"
 251              ,@(if (string-prefix? "x86_64" (or (%current-target-system)
 252                                                 (%current-system)))
 253                    '("-DCPU_DISPATCH_REQUIRE=SSE3,SSSE3,SSE4_1,SSE4_2,AVX,AVX2")
 254                    '())
 255
 256              "-DBUILD_PERF_TESTS=OFF"
 257              "-DBUILD_TESTS=ON"
 258
 259              (string-append "-DOPENCV_EXTRA_MODULES_PATH=" (getcwd)
 260                             "/opencv-contrib/opencv_contrib-" ,version
 261                             "/modules")
 262
 263              ;;Define test data:
 264              (string-append "-DOPENCV_TEST_DATA_PATH=" (getcwd)
 265                             "/opencv-extra/opencv_extra-" ,version
 266                             "/testdata")
 267
 268              ;; Is ON by default and would try to rebuild 3rd-party protobuf,
 269              ;; which we had removed, which would lead to an error:
 270              "-DBUILD_PROTOBUF=OFF"
 271
 272              ;; Rebuild protobuf files, because we have a slightly different
 273              ;; version than the included one. If we would not update, we
 274              ;; would get a compile error later:
 275              "-DPROTOBUF_UPDATE_FILES=ON"
 276
 277              ;; xfeatures2d disabled, because it downloads extra binaries from
 278              ;; https://github.com/opencv/opencv_3rdparty
 279              ;; defined in xfeatures2d/cmake/download_{vgg|bootdesc}.cmake
 280              ;; Cmp this bug entry:
 281              ;; https://github.com/opencv/opencv_contrib/issues/1131
 282              "-DBUILD_opencv_xfeatures2d=OFF")
 283        #:phases
 284        (modify-phases %standard-phases
 285          (add-after 'unpack 'disable-broken-tests
 286            (lambda _
 287              ;; These tests fails with:
 288              ;; vtkXOpenGLRenderWindow (0x723990): Could not find a decent config
 289              ;; I think we have no OpenGL support with the Xvfb.
 290              (substitute* '("modules/viz/test/test_tutorial3.cpp"
 291                             "modules/viz/test/test_main.cpp"
 292                             "modules/viz/test/tests_simple.cpp"
 293                             "modules/viz/test/test_viz3d.cpp")
 294                (("(TEST\\(Viz, )([a-z].*\\).*)" all pre post)
 295                 (string-append pre "DISABLED_" post)))
 296
 297              ;; This one fails with "unknown file: Failure"
 298              ;; But I couldn't figure out which file was missing:
 299              (substitute* (list (string-append
 300                                  "../opencv-contrib/opencv_contrib-"
 301                                  ,version
 302                                  "/modules/face/test/test_face_align.cpp"))
 303                (("(TEST\\(CV_Face_FacemarkKazemi, )(can_detect_landmarks\\).*)"
 304                  all pre post)
 305                 (string-append pre "DISABLED_" post)))
 306
 307              ;; Failure reason: Bad accuracy
 308              ;; Incorrect count of accurate poses [2nd case]: 90.000000 / 94.000000
 309              (substitute* (list (string-append
 310                                  "../opencv-contrib/opencv_contrib-"
 311                                  ,version
 312                                  "/modules/rgbd/test/test_odometry.cpp"))
 313                (("(TEST\\(RGBD_Odometry_Rgbd, )(algorithmic\\).*)" all pre post)
 314                 (string-append pre "DISABLED_" post)))
 315              #t))
 316
 317          ;; Idea copied from ldc.scm (ldc-bootstrap):
 318          (add-after 'unpack 'unpack-submodule-sources
 319            (lambda* (#:key inputs #:allow-other-keys)
 320              (mkdir "../opencv-extra")
 321              (mkdir "../opencv-contrib")
 322              (let ((unpack (lambda (source target)
 323                              (with-directory-excursion target
 324                                (apply invoke "unzip"
 325                                       (list (assoc-ref inputs source)))))))
 326                (unpack "opencv-extra" "../opencv-extra")
 327                (unpack "opencv-contrib" "../opencv-contrib"))))
 328
 329          (add-after 'set-paths 'add-ilmbase-include-path
 330            (lambda* (#:key inputs #:allow-other-keys)
 331            ;; OpenEXR propagates ilmbase, but its include files do not appear
 332            ;; in the CPATH, so we need to add "$ilmbase/include/OpenEXR/" to
 333            ;; the CPATH to satisfy the dependency on "ImathVec.h".
 334            (setenv "CPATH"
 335                    (string-append (assoc-ref inputs "ilmbase")
 336                                   "/include/OpenEXR"
 337                                   ":" (or (getenv "CPATH") "")))
 338            #t))
 339        (add-before 'check 'start-xserver
 340          (lambda* (#:key inputs #:allow-other-keys)
 341            (let ((xorg-server (assoc-ref inputs "xorg-server"))
 342                  (disp ":1"))
 343              (setenv "HOME" (getcwd))
 344              (setenv "DISPLAY" disp)
 345              ;; There must be a running X server and make check doesn't start one.
 346              ;; Therefore we must do it.
 347              (zero? (system (format #f "~a/bin/Xvfb ~a &" xorg-server disp)))))))))
 348     (native-inputs
 349      `(("unzip" ,unzip)
 350        ("pkg-config" ,pkg-config)
 351        ("xorg-server" ,xorg-server) ; For running the tests
 352        ("opencv-extra"
 353         ,(origin
 354            (method url-fetch)
 355            (uri (string-append "https://codeload.github.com/"
 356                                "opencv/opencv_extra/zip/" version))
 357            (file-name (string-append "opencv-extra-" version ".zip"))
 358            (sha256
 359             (base32 "0yd1vidzbg6himxyh4yzivywijg8548kfmcn421khabnipm7l74y"))))
 360        ("opencv-contrib"
 361         ,(origin
 362            (method url-fetch)
 363            (uri (string-append "https://codeload.github.com/"
 364                                "opencv/opencv_contrib/zip/" version))
 365            (file-name (string-append "opencv-contrib-" version ".zip"))
 366            (sha256
 367            (base32 "0j0ci6ia1qwklp9hq07ypl0vkngj1wrgh6n98n657m5d0pyp4m0g"))))))
 368     (inputs `(("libjpeg" ,libjpeg)
 369               ("libpng" ,libpng)
 370               ("jasper" ,jasper)
 371               ;; ffmpeg 4.0 causes core dumps in tests.
 372               ("ffmpeg" ,ffmpeg-3.4)
 373               ("libtiff" ,libtiff)
 374               ("hdf5" ,hdf5)
 375               ("libgphoto2" ,libgphoto2)
 376               ("libwebp" ,libwebp)
 377               ("zlib" ,zlib)
 378               ("gtkglext" ,gtkglext)
 379               ("openexr" ,openexr)
 380               ("ilmbase" ,ilmbase)
 381               ("gtk+" ,gtk+-2)
 382               ("python-numpy" ,python-numpy)
 383               ("protobuf" ,protobuf)
 384               ("vtk" ,vtk)
 385               ("python" ,python)))
 386     ;; These three CVEs are not a problem of OpenCV, see:
 387     ;; https://github.com/opencv/opencv/issues/10998
 388     (properties '((lint-hidden-cve . ("CVE-2018-7712"
 389                                       "CVE-2018-7713"
 390                                       "CVE-2018-7714"))))
 391     (synopsis "Computer vision library")
 392     (description "OpenCV is a library aimed at
 393 real-time computer vision, including several hundred computer
 394 vision algorithms.  It can be used to do things like:
 395
 396 @itemize
 397 @item image and video input and output
 398 @item image and video processing
 399 @item displaying
 400 @item feature recognition
 401 @item segmentation
 402 @item facial recognition
 403 @item stereo vision
 404 @item structure from motion
 405 @item augmented reality
 406 @item machine learning
 407 @end itemize\n")
 408     (home-page "https://opencv.org/")
 409     (license license:bsd-3)))
 410
 411 (define-public vips
 412   (package
 413     (name "vips")
 414     (version "8.7.1")
 415     (source (origin
 416               (method url-fetch)
 417               (uri (string-append
 418                     "https://github.com/libvips/libvips/releases/download/v"
 419                     version "/vips-" version ".tar.gz"))
 420               (sha256
 421                (base32 "1w3b90pdw7nj2p0gb4f96h6zhmga513f968ldfhz1rkhg7y81c0s"))))
 422     (build-system gnu-build-system)
 423     (native-inputs
 424      `(("pkg-config" ,pkg-config)
 425        ("gobject-introspection" ,gobject-introspection)))
 426     (inputs
 427      `(("glib" ,glib)
 428        ("libjpeg" ,libjpeg)
 429        ("libpng" ,libpng)
 430        ("librsvg" ,librsvg)
 431        ("libtiff" ,libtiff)
 432        ("libexif" ,libexif)
 433        ("giflib" ,giflib)
 434        ("libgsf" ,libgsf)
 435        ("fftw" ,fftw)
 436        ("poppler" ,poppler)
 437        ("pango" ,pango)
 438        ("lcms" ,lcms)
 439        ("matio" ,matio)
 440        ("libwebp" ,libwebp)
 441        ("niftilib" ,niftilib)
 442        ("openexr" ,openexr)
 443        ("orc" ,orc)
 444        ("imagemagick" ,imagemagick)
 445        ("libxml2" ,libxml2)
 446        ("expat" ,expat)
 447        ("hdf5" ,hdf5)))
 448     (home-page "https://libvips.github.io/libvips/")
 449     (synopsis "Image processing system")
 450     (description
 451      "vips is a demand-driven, horizontally threaded image processing library.")
 452     (license license:lgpl2.1+)))
 453
 454 (define-public nip2
 455   (package
 456     (name "nip2")
 457     (version "8.7.0")
 458     (source
 459      (origin
 460        (method url-fetch)
 461        (uri (string-append "https://github.com/libvips/nip2/releases/download/v"
 462                            version "/nip2-" version ".tar.gz" ))
 463        (sha256
 464         (base32 "08dxfds4n1vxdilxcw01741a2r6fxyhawi656b7f0hy6znnkbsbc"))))
 465     (build-system gnu-build-system)
 466     (arguments
 467      `(#:phases
 468        (modify-phases %standard-phases
 469          ;; test_conv.ws keep failing so disabling for now
 470          (add-after 'unpack 'disable-test-conv
 471            (lambda _
 472              (delete-file "test/workspaces/test_conv.ws")
 473              #t))
 474          (add-before 'check 'set-home
 475            (lambda _
 476              (setenv "HOME" "/tmp") #t)))))
 477     (inputs
 478      `(("vips" ,vips)
 479        ("glib" ,glib)
 480        ("libtiff" ,libtiff)
 481        ("gtk+-2" ,gtk+-2)
 482        ("libxml2" ,libxml2)
 483        ("libexif" ,libexif)
 484        ("libjpeg" ,libjpeg)                       ;required by vips.pc
 485        ("librsvg" ,librsvg)
 486        ("fftw" ,fftw)
 487        ("libgsf" ,libgsf)
 488        ("imagemagick" ,imagemagick)
 489        ("orc" ,orc)
 490        ("matio" ,matio)
 491        ("lcms" ,lcms)
 492        ("libwebp" ,libwebp)
 493        ("openexr" ,openexr)
 494        ("poppler" ,poppler)
 495        ("gsl" ,gsl)))
 496     (native-inputs
 497      `(("flex" ,flex)
 498        ("bison" ,bison)
 499        ("pkg-config" ,pkg-config)))
 500     (home-page "https://github.com/libvips/nip2")
 501     (synopsis "Spreadsheet-like GUI for libvips")
 502     (description "This package provide a graphical user interface (GUI) for
 503 the VIPS image processing library.  It's a little like a spreadsheet: you
 504 create a set of formula connecting your objects together, and on a change nip2
 505 recalculates.")
 506     (license license:gpl2+)))