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 git-download)
  33   #:use-module (guix build-system cmake)
  34   #:use-module (guix build-system gnu)
  35   #:use-module (gnu packages)
  36   #:use-module (gnu packages algebra)
  37   #:use-module (gnu packages bison)
  38   #:use-module (gnu packages boost)
  39   #:use-module (gnu packages compression)
  40   #:use-module (gnu packages documentation)
  41   #:use-module (gnu packages flex)
  42   #:use-module (gnu packages fontutils)
  43   #:use-module (gnu packages ghostscript)
  44   #:use-module (gnu packages gl)
  45   #:use-module (gnu packages glib)
  46   #:use-module (gnu packages gnome)
  47   #:use-module (gnu packages graphics)
  48   #:use-module (gnu packages graphviz)
  49   #:use-module (gnu packages gstreamer)
  50   #:use-module (gnu packages gtk)
  51   #:use-module (gnu packages image)
  52   #:use-module (gnu packages imagemagick)
  53   #:use-module (gnu packages maths)
  54   #:use-module (gnu packages pdf)
  55   #:use-module (gnu packages perl)
  56   #:use-module (gnu packages photo)
  57   #:use-module (gnu packages pkg-config)
  58   #:use-module (gnu packages protobuf)
  59   #:use-module (gnu packages python)
  60   #:use-module (gnu packages python-xyz)
  61   #:use-module (gnu packages serialization)
  62   #:use-module (gnu packages video)
  63   #:use-module (gnu packages xiph)
  64   #:use-module (gnu packages xml)
  65   #:use-module (gnu packages xorg)
  66   #:use-module (ice-9 match))
  67
  68 ;; We use the latest snapshot of this package because the latest release is
  69 ;; from 2011 and has known vulnerabilities that cannot easily be fixed by
  70 ;; applying patches.
  71 (define-public dcmtk
  72   (package
  73     (name "dcmtk")
  74     (version "3.6.1_20170228")
  75     (source (origin
  76               (method url-fetch)
  77               (uri (string-append "ftp://dicom.offis.de/pub/dicom/offis/"
  78                                   "software/dcmtk/snapshot/dcmtk-"
  79                                   version ".tar.gz"))
  80               (sha256
  81                (base32
  82                 "04cwfx8yrscqcd59mxk2fh6314ckayi9cp68iql5a57pf2pg5qld"))))
  83     (build-system gnu-build-system)
  84     (inputs
  85      `(("libtiff" ,libtiff)
  86        ("libpng" ,libpng)
  87        ("doxygen" ,doxygen)
  88        ("zlib" ,zlib)))
  89     (native-inputs
  90      `(("perl" ,perl)))
  91     (home-page "http://dcmtk.org")
  92     (synopsis "Libraries and programs implementing parts of the DICOM standard")
  93     (description "DCMTK is a collection of libraries and applications
  94 implementing large parts the DICOM standard.  It includes software for
  95 examining, constructing and converting DICOM image files, handling offline
  96 media, sending and receiving images over a network connection, as well as
  97 demonstrative image storage and worklist servers.")
  98     (license (license:fsf-free
  99               "file://COPYRIGHT"
 100               "A union of the Apache 2.0 licence and various non-copyleft
 101 licences similar to the Modified BSD licence."))))
 102
 103 (define-public mia
 104   (package
 105     (name "mia")
 106     (version "2.4.6")
 107     (source (origin
 108               (method url-fetch)
 109               (uri (string-append "mirror://sourceforge/mia/mia/"
 110                                   (version-major+minor version)
 111                                   "/mia-" version ".tar.xz"))
 112               (sha256
 113                (base32
 114                 "0j4nd5z7i3v199jh7hqqhwd4g7snchizkc7rhzanpvngqg91m1pb"))))
 115     (build-system cmake-build-system)
 116     (arguments
 117      `(#:configure-flags
 118        (list "-DMIA_CREATE_NIPYPE_INTERFACES=0"
 119              "-DCMAKE_CXX_FLAGS=-fpermissive")))
 120     (inputs
 121      `(("boost" ,boost)
 122        ("dcmtk" ,dcmtk)
 123        ("doxygen" ,doxygen)
 124        ("eigen" ,eigen)
 125        ("fftw" ,fftw)
 126        ("fftwf" ,fftwf)
 127        ("gsl" ,gsl)
 128        ("gts" ,gts)
 129        ("hdf5" ,hdf5)
 130        ("itpp" ,itpp)
 131        ("libjpeg" ,libjpeg)
 132        ("libpng" ,libpng)
 133        ("libtiff" ,libtiff)
 134        ("libxml" ,libxml2)
 135        ("libxml++" ,libxml++)
 136        ("maxflow" ,maxflow)
 137        ("niftilib" ,niftilib)
 138        ("nlopt" ,nlopt)
 139        ("openexr" ,openexr)
 140        ("python-lxml" ,python2-lxml)
 141        ("vtk" ,vtk)))
 142     (native-inputs
 143      `(("pkg-config" ,pkg-config)
 144        ("python" ,python-2)))
 145     (home-page "http://mia.sourceforge.net")
 146     (synopsis "Toolkit for gray scale medical image analysis")
 147     (description "MIA provides a combination of command line tools, plug-ins,
 148 and libraries that make it possible run image processing tasks interactively
 149 in a command shell and to prototype using the shell's scripting language.  It
 150 is built around a plug-in structure that makes it easy to add functionality
 151 without compromising the original code base and it makes use of a wide variety
 152 of external libraries that provide additional functionality.")
 153     (license license:gpl3+)))
 154
 155 (define-public vtk
 156   (package
 157     (name "vtk")
 158     (version "8.2.0")
 159     (source (origin
 160               (method url-fetch)
 161               (uri (string-append "https://vtk.org/files/release/"
 162                                   (version-major+minor version)
 163                                   "/VTK-" version ".tar.gz"))
 164               (sha256
 165                (base32
 166                 "1fspgp8k0myr6p2a6wkc21ldcswb4bvmb484m12mxgk1a9vxrhrl"))))
 167     (build-system cmake-build-system)
 168     (arguments
 169      '(#:build-type "Release"           ;Build without '-g' to save space.
 170        ;; -DVTK_USE_SYSTEM_NETCDF:BOOL=TRUE requires netcdf_cxx
 171        #:configure-flags '("-DVTK_USE_SYSTEM_EXPAT:BOOL=TRUE"
 172                            "-DVTK_USE_SYSTEM_FREETYPE:BOOL=TRUE"
 173                            "-DVTK_USE_SYSTEM_HDF5:BOOL=TRUE"
 174                            "-DVTK_USE_SYSTEM_JPEG:BOOL=TRUE"
 175                            "-DVTK_USE_SYSTEM_JSONCPP:BOOL=TRUE"
 176                            "-DVTK_USE_SYSTEM_LIBXML2:BOOL=TRUE"
 177                            "-DVTK_USE_SYSTEM_OGGTHEORA:BOOL=TRUE"
 178                            "-DVTK_USE_SYSTEM_PNG:BOOL=TRUE"
 179                            "-DVTK_USE_SYSTEM_TIFF:BOOL=TRUE"
 180                            "-DVTK_USE_SYSTEM_ZLIB:BOOL=TRUE")
 181        #:tests? #f))                              ;XXX: no "test" target
 182     (inputs
 183      `(("libXt" ,libxt)
 184        ("xorgproto" ,xorgproto)
 185        ("libX11" ,libx11)
 186        ("libxml2" ,libxml2)
 187        ("mesa" ,mesa)
 188        ("glu" ,glu)
 189        ("expat" ,expat)
 190        ("freetype" ,freetype)
 191        ("hdf5" ,hdf5)
 192        ("jpeg" ,libjpeg)
 193        ("jsoncpp" ,jsoncpp)
 194        ("libogg" ,libogg)
 195        ("libtheora" ,libtheora)
 196        ("png" ,libpng)
 197        ("tiff" ,libtiff)
 198        ("zlib" ,zlib)))
 199     (home-page "https://vtk.org/")
 200     (synopsis "Libraries for 3D computer graphics")
 201     (description
 202      "The Visualization Toolkit (VTK) is a C++ library for 3D computer graphics,
 203 image processing and visualization.  It supports a wide variety of
 204 visualization algorithms including: scalar, vector, tensor, texture, and
 205 volumetric methods; and advanced modeling techniques such as: implicit
 206 modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay
 207 triangulation.  VTK has an extensive information visualization framework, has
 208 a suite of 3D interaction widgets, supports parallel processing, and
 209 integrates with various databases on GUI toolkits such as Qt and Tk.")
 210     (license license:bsd-3)))
 211
 212 (define-public opencv
 213   (package
 214     (name "opencv")
 215     (version "3.4.3")
 216     (source (origin
 217               (method git-fetch)
 218               (uri (git-reference
 219                      (url "https://github.com/opencv/opencv")
 220                      (commit version)))
 221               (file-name (git-file-name name version))
 222               (sha256
 223                (base32
 224                 "06bc61r8myym4s8im10brdjfg4wxkrvsbhhl7vr1msdan2xddzi3"))
 225               (modules '((guix build utils)))
 226               (snippet
 227                '(begin
 228                   ;; Remove external libraries. We have all available in Guix:
 229                   (delete-file-recursively "3rdparty")
 230
 231                   ;; Milky icon set is non-free:
 232                   (delete-file-recursively "modules/highgui/src/files_Qt/Milky")
 233
 234                   ;; Some jars found:
 235                   (for-each delete-file
 236                             '("modules/java/test/pure_test/lib/junit-4.11.jar"
 237                               "samples/java/sbt/sbt/sbt-launch.jar"))
 238                   #t))))
 239     (build-system cmake-build-system)
 240     (arguments
 241      `(#:configure-flags
 242        (list "-DWITH_IPP=OFF"
 243              "-DWITH_ITT=OFF"
 244              "-DWITH_CAROTENE=OFF" ; only visible on arm/aarch64
 245              "-DENABLE_PRECOMPILED_HEADERS=OFF"
 246
 247              ;; CPU-Features:
 248              ;; See cmake/OpenCVCompilerOptimizations.cmake
 249              ;; (CPU_ALL_OPTIMIZATIONS) for a list of all optimizations
 250              ;; BASELINE is the minimum optimization all CPUs must support
 251              ;;
 252              ;; DISPATCH is the list of optional dispatches.
 253              "-DCPU_BASELINE=SSE2"
 254
 255              ,@(match (%current-system)
 256                  ("x86_64-linux"
 257                   '("-DCPU_DISPATCH=NEON;VFPV3;FP16;SSE;SSE2;SSE3;SSSE3;SSE4_1;SSE4_2;POPCNT;AVX;FP16;AVX2;FMA3;AVX_512F;AVX512_SKX"
 258                     "-DCPU_DISPATCH_REQUIRE=SSE3,SSSE3,SSE4_1,SSE4_2,AVX,AVX2"))
 259                  ("armhf-linux"
 260                   '("-DCPU_BASELINE_DISABLE=NEON")) ; causes build failures
 261                  ("aarch64-linux"
 262                   '("-DCPU_BASELINE=NEON"
 263                     "-DCPU_DISPATCH=NEON;VFPV3;FP16"))
 264                  (_ '()))
 265
 266              "-DBUILD_PERF_TESTS=OFF"
 267              "-DBUILD_TESTS=ON"
 268
 269              (string-append "-DOPENCV_EXTRA_MODULES_PATH=" (getcwd)
 270                             "/opencv-contrib/modules")
 271
 272              ;;Define test data:
 273              (string-append "-DOPENCV_TEST_DATA_PATH=" (getcwd)
 274                             "/opencv-extra/testdata")
 275
 276              ;; Is ON by default and would try to rebuild 3rd-party protobuf,
 277              ;; which we had removed, which would lead to an error:
 278              "-DBUILD_PROTOBUF=OFF"
 279
 280              ;; Rebuild protobuf files, because we have a slightly different
 281              ;; version than the included one. If we would not update, we
 282              ;; would get a compile error later:
 283              "-DPROTOBUF_UPDATE_FILES=ON"
 284
 285              ;; xfeatures2d disabled, because it downloads extra binaries from
 286              ;; https://github.com/opencv/opencv_3rdparty
 287              ;; defined in xfeatures2d/cmake/download_{vgg|bootdesc}.cmake
 288              ;; Cmp this bug entry:
 289              ;; https://github.com/opencv/opencv_contrib/issues/1131
 290              "-DBUILD_opencv_xfeatures2d=OFF")
 291        #:phases
 292        (modify-phases %standard-phases
 293          (add-after 'unpack 'disable-broken-tests
 294            (lambda _
 295              ;; These tests fails with:
 296              ;; vtkXOpenGLRenderWindow (0x723990): Could not find a decent config
 297              ;; I think we have no OpenGL support with the Xvfb.
 298              (substitute* '("modules/viz/test/test_tutorial3.cpp"
 299                             "modules/viz/test/test_main.cpp"
 300                             "modules/viz/test/tests_simple.cpp"
 301                             "modules/viz/test/test_viz3d.cpp")
 302                (("(TEST\\(Viz, )([a-z].*\\).*)" all pre post)
 303                 (string-append pre "DISABLED_" post)))
 304
 305              ;; This one fails with "unknown file: Failure"
 306              ;; But I couldn't figure out which file was missing:
 307              (substitute* "../opencv-contrib/modules/face/test/test_face_align.cpp"
 308                (("(TEST\\(CV_Face_FacemarkKazemi, )(can_detect_landmarks\\).*)"
 309                  all pre post)
 310                 (string-append pre "DISABLED_" post)))
 311
 312              ;; Failure reason: Bad accuracy
 313              ;; Incorrect count of accurate poses [2nd case]: 90.000000 / 94.000000
 314              (substitute* "../opencv-contrib/modules/rgbd/test/test_odometry.cpp"
 315                (("(TEST\\(RGBD_Odometry_Rgbd, )(algorithmic\\).*)" all pre post)
 316                 (string-append pre "DISABLED_" post)))
 317              #t))
 318
 319          (add-after 'unpack 'unpack-submodule-sources
 320            (lambda* (#:key inputs #:allow-other-keys)
 321              (mkdir "../opencv-extra")
 322              (mkdir "../opencv-contrib")
 323              (copy-recursively (assoc-ref inputs "opencv-extra")
 324                                "../opencv-extra")
 325              (invoke "tar" "xvf"
 326                      (assoc-ref inputs "opencv-contrib")
 327                      "--strip-components=1"
 328                      "-C" "../opencv-contrib")))
 329
 330          (add-after 'set-paths 'add-ilmbase-include-path
 331            (lambda* (#:key inputs #:allow-other-keys)
 332            ;; OpenEXR propagates ilmbase, but its include files do not appear
 333            ;; in the CPATH, so we need to add "$ilmbase/include/OpenEXR/" to
 334            ;; the CPATH to satisfy the dependency on "ImathVec.h".
 335            (setenv "CPATH"
 336                    (string-append (assoc-ref inputs "ilmbase")
 337                                   "/include/OpenEXR"
 338                                   ":" (or (getenv "CPATH") "")))
 339            #t))
 340        (add-before 'check 'start-xserver
 341          (lambda* (#:key inputs #:allow-other-keys)
 342            (let ((xorg-server (assoc-ref inputs "xorg-server"))
 343                  (disp ":1"))
 344              (setenv "HOME" (getcwd))
 345              (setenv "DISPLAY" disp)
 346              ;; There must be a running X server and make check doesn't start one.
 347              ;; Therefore we must do it.
 348              (zero? (system (format #f "~a/bin/Xvfb ~a &" xorg-server disp)))))))))
 349     (native-inputs
 350      `(("pkg-config" ,pkg-config)
 351        ("xorg-server" ,xorg-server) ; For running the tests
 352        ("opencv-extra"
 353         ,(origin
 354            (method git-fetch)
 355            (uri (git-reference
 356                   (url "https://github.com/opencv/opencv_extra")
 357                   (commit version)))
 358            (file-name (git-file-name "opencv_extra" version))
 359            (sha256
 360             (base32 "08p5xnq8n1jw8svvz0fnirfg7q8dm3p4a5dl7527s5xj0f9qn7lp"))))
 361        ("opencv-contrib"
 362         ,(origin
 363            (method git-fetch)
 364            (uri (git-reference
 365                   (url "https://github.com/opencv/opencv_contrib")
 366                   (commit version)))
 367            (file-name (git-file-name "opencv_contrib" version))
 368            (patches (search-patches "opencv-rgbd-aarch64-test-fix.patch"))
 369            (sha256
 370             (base32 "1f334glf39nk42mpqq6j732h3ql2mpz89jd4mcl678s8n73nfjh2"))))))
 371     (inputs `(("libjpeg" ,libjpeg)
 372               ("libpng" ,libpng)
 373               ("jasper" ,jasper)
 374               ;; ffmpeg 4.0 causes core dumps in tests.
 375               ("ffmpeg" ,ffmpeg-3.4)
 376               ("libtiff" ,libtiff)
 377               ("hdf5" ,hdf5)
 378               ("libgphoto2" ,libgphoto2)
 379               ("libwebp" ,libwebp)
 380               ("zlib" ,zlib)
 381               ("gtkglext" ,gtkglext)
 382               ("openexr" ,openexr)
 383               ("ilmbase" ,ilmbase)
 384               ("gtk+" ,gtk+-2)
 385               ("python-numpy" ,python-numpy)
 386               ("protobuf" ,protobuf)
 387               ("vtk" ,vtk)
 388               ("python" ,python)))
 389     ;; These three CVEs are not a problem of OpenCV, see:
 390     ;; https://github.com/opencv/opencv/issues/10998
 391     (properties '((lint-hidden-cve . ("CVE-2018-7712"
 392                                       "CVE-2018-7713"
 393                                       "CVE-2018-7714"))))
 394     (synopsis "Computer vision library")
 395     (description "OpenCV is a library aimed at
 396 real-time computer vision, including several hundred computer
 397 vision algorithms.  It can be used to do things like:
 398
 399 @itemize
 400 @item image and video input and output
 401 @item image and video processing
 402 @item displaying
 403 @item feature recognition
 404 @item segmentation
 405 @item facial recognition
 406 @item stereo vision
 407 @item structure from motion
 408 @item augmented reality
 409 @item machine learning
 410 @end itemize\n")
 411     (home-page "https://opencv.org/")
 412     (license license:bsd-3)))
 413
 414 (define-public vips
 415   (package
 416     (name "vips")
 417     (version "8.7.1")
 418     (source (origin
 419               (method url-fetch)
 420               (uri (string-append
 421                     "https://github.com/libvips/libvips/releases/download/v"
 422                     version "/vips-" version ".tar.gz"))
 423               (sha256
 424                (base32 "1w3b90pdw7nj2p0gb4f96h6zhmga513f968ldfhz1rkhg7y81c0s"))))
 425     (build-system gnu-build-system)
 426     (native-inputs
 427      `(("pkg-config" ,pkg-config)
 428        ("gobject-introspection" ,gobject-introspection)))
 429     (inputs
 430      `(("glib" ,glib)
 431        ("libjpeg" ,libjpeg)
 432        ("libpng" ,libpng)
 433        ("librsvg" ,librsvg)
 434        ("libtiff" ,libtiff)
 435        ("libexif" ,libexif)
 436        ("giflib" ,giflib)
 437        ("libgsf" ,libgsf)
 438        ("fftw" ,fftw)
 439        ("poppler" ,poppler)
 440        ("pango" ,pango)
 441        ("lcms" ,lcms)
 442        ("matio" ,matio)
 443        ("libwebp" ,libwebp)
 444        ("niftilib" ,niftilib)
 445        ("openexr" ,openexr)
 446        ("orc" ,orc)
 447        ("imagemagick" ,imagemagick)
 448        ("libxml2" ,libxml2)
 449        ("expat" ,expat)
 450        ("hdf5" ,hdf5)))
 451     (home-page "https://libvips.github.io/libvips/")
 452     (synopsis "Image processing system")
 453     (description
 454      "vips is a demand-driven, horizontally threaded image processing library.")
 455     (license license:lgpl2.1+)))
 456
 457 (define-public nip2
 458   (package
 459     (name "nip2")
 460     (version "8.7.0")
 461     (source
 462      (origin
 463        (method url-fetch)
 464        (uri (string-append "https://github.com/libvips/nip2/releases/download/v"
 465                            version "/nip2-" version ".tar.gz" ))
 466        (sha256
 467         (base32 "08dxfds4n1vxdilxcw01741a2r6fxyhawi656b7f0hy6znnkbsbc"))))
 468     (build-system gnu-build-system)
 469     (arguments
 470      `(#:phases
 471        (modify-phases %standard-phases
 472          ;; test_conv.ws keep failing so disabling for now
 473          (add-after 'unpack 'disable-test-conv
 474            (lambda _
 475              (delete-file "test/workspaces/test_conv.ws")
 476              #t))
 477          (add-before 'check 'set-home
 478            (lambda _
 479              (setenv "HOME" "/tmp") #t)))))
 480     (inputs
 481      `(("vips" ,vips)
 482        ("glib" ,glib)
 483        ("libtiff" ,libtiff)
 484        ("gtk+-2" ,gtk+-2)
 485        ("libxml2" ,libxml2)
 486        ("libexif" ,libexif)
 487        ("libjpeg" ,libjpeg)                       ;required by vips.pc
 488        ("librsvg" ,librsvg)
 489        ("fftw" ,fftw)
 490        ("libgsf" ,libgsf)
 491        ("imagemagick" ,imagemagick)
 492        ("orc" ,orc)
 493        ("matio" ,matio)
 494        ("lcms" ,lcms)
 495        ("libwebp" ,libwebp)
 496        ("openexr" ,openexr)
 497        ("poppler" ,poppler)
 498        ("gsl" ,gsl)))
 499     (native-inputs
 500      `(("flex" ,flex)
 501        ("bison" ,bison)
 502        ("pkg-config" ,pkg-config)))
 503     (home-page "https://github.com/libvips/nip2")
 504     (synopsis "Spreadsheet-like GUI for libvips")
 505     (description "This package provide a graphical user interface (GUI) for
 506 the VIPS image processing library.  It's a little like a spreadsheet: you
 507 create a set of formula connecting your objects together, and on a change nip2
 508 recalculates.")
 509     (license license:gpl2+)))