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, 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 ;;;
  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 tls)
  63   #:use-module (gnu packages video)
  64   #:use-module (gnu packages xiph)
  65   #:use-module (gnu packages xml)
  66   #:use-module (gnu packages xorg)
  67   #:use-module (ice-9 match))
  68
  69 (define-public dcmtk
  70   (package
  71     (name "dcmtk")
  72     (version "3.6.4")
  73     (source
  74      (origin
  75        (method url-fetch)
  76        (uri
  77         (string-append "ftp://dicom.offis.de/pub/dicom/offis/software/dcmtk/"
  78                        "dcmtk" (string-join (string-split version #\.) "")
  79                        "/dcmtk-" version ".tar.gz"))
  80        (sha256
  81         (base32 "1h22z8g0kmvhg8lgkbikyzyphhvxvq6018a00yd6i4g0z9ag6gx9"))))
  82     (build-system cmake-build-system)
  83     (inputs
  84      `(;; Our ICU is too recent: “error: ‘UChar’ does not name a type“.
  85        ;; ("icu4c" ,icu4c)
  86        ("libjpeg" ,libjpeg)
  87        ("libpng" ,libpng)
  88        ("libtiff" ,libtiff)
  89        ("libxml2" ,libxml2)
  90        ("openssl" ,openssl)
  91        ("zlib" ,zlib)))
  92     (native-inputs
  93      `(("doxygen" ,doxygen)))           ; for HTML documentation
  94     (home-page "https://dcmtk.org")
  95     (synopsis "Libraries and programs implementing parts of the DICOM standard")
  96     (description "DCMTK is a collection of libraries and applications
  97 implementing large parts the DICOM standard.  It includes software for
  98 examining, constructing and converting DICOM image files, handling offline
  99 media, sending and receiving images over a network connection, as well as
 100 demonstrative image storage and worklist servers.")
 101     (license (license:fsf-free
 102               "file://COPYRIGHT"
 103               "A union of the Apache 2.0 licence and various non-copyleft
 104 licences similar to the Modified BSD licence."))))
 105
 106 (define-public mia
 107   (package
 108     (name "mia")
 109     (version "2.4.6")
 110     (source (origin
 111               (method url-fetch)
 112               (uri (string-append "mirror://sourceforge/mia/mia/"
 113                                   (version-major+minor version)
 114                                   "/mia-" version ".tar.xz"))
 115               (sha256
 116                (base32
 117                 "0j4nd5z7i3v199jh7hqqhwd4g7snchizkc7rhzanpvngqg91m1pb"))))
 118     (build-system cmake-build-system)
 119     (arguments
 120      `(#:configure-flags
 121        (list "-DMIA_CREATE_NIPYPE_INTERFACES=0"
 122              "-DCMAKE_CXX_FLAGS=-fpermissive")))
 123     (inputs
 124      `(("boost" ,boost)
 125        ("dcmtk" ,dcmtk)
 126        ("doxygen" ,doxygen)
 127        ("eigen" ,eigen)
 128        ("fftw" ,fftw)
 129        ("fftwf" ,fftwf)
 130        ("gsl" ,gsl)
 131        ("gts" ,gts)
 132        ("hdf5" ,hdf5)
 133        ("itpp" ,itpp)
 134        ("libjpeg" ,libjpeg)
 135        ("libpng" ,libpng)
 136        ("libtiff" ,libtiff)
 137        ("libxml" ,libxml2)
 138        ("libxml++" ,libxml++)
 139        ("maxflow" ,maxflow)
 140        ("niftilib" ,niftilib)
 141        ("nlopt" ,nlopt)
 142        ("openexr" ,openexr)
 143        ("python-lxml" ,python2-lxml)
 144        ("vtk" ,vtk)))
 145     (native-inputs
 146      `(("pkg-config" ,pkg-config)
 147        ("python" ,python-2)))
 148     (home-page "http://mia.sourceforge.net")
 149     (synopsis "Toolkit for gray scale medical image analysis")
 150     (description "MIA provides a combination of command line tools, plug-ins,
 151 and libraries that make it possible run image processing tasks interactively
 152 in a command shell and to prototype using the shell's scripting language.  It
 153 is built around a plug-in structure that makes it easy to add functionality
 154 without compromising the original code base and it makes use of a wide variety
 155 of external libraries that provide additional functionality.")
 156     (license license:gpl3+)))
 157
 158 (define-public vtk
 159   (package
 160     (name "vtk")
 161     (version "8.2.0")
 162     (source (origin
 163               (method url-fetch)
 164               (uri (string-append "https://vtk.org/files/release/"
 165                                   (version-major+minor version)
 166                                   "/VTK-" version ".tar.gz"))
 167               (sha256
 168                (base32
 169                 "1fspgp8k0myr6p2a6wkc21ldcswb4bvmb484m12mxgk1a9vxrhrl"))))
 170     (build-system cmake-build-system)
 171     (arguments
 172      '(#:build-type "Release"           ;Build without '-g' to save space.
 173        ;; -DVTK_USE_SYSTEM_NETCDF:BOOL=TRUE requires netcdf_cxx
 174        #:configure-flags '("-DVTK_USE_SYSTEM_EXPAT:BOOL=TRUE"
 175                            "-DVTK_USE_SYSTEM_FREETYPE:BOOL=TRUE"
 176                            "-DVTK_USE_SYSTEM_HDF5:BOOL=TRUE"
 177                            "-DVTK_USE_SYSTEM_JPEG:BOOL=TRUE"
 178                            "-DVTK_USE_SYSTEM_JSONCPP:BOOL=TRUE"
 179                            "-DVTK_USE_SYSTEM_LIBXML2:BOOL=TRUE"
 180                            "-DVTK_USE_SYSTEM_OGGTHEORA:BOOL=TRUE"
 181                            "-DVTK_USE_SYSTEM_PNG:BOOL=TRUE"
 182                            "-DVTK_USE_SYSTEM_TIFF:BOOL=TRUE"
 183                            "-DVTK_USE_SYSTEM_ZLIB:BOOL=TRUE")
 184        #:tests? #f))                              ;XXX: no "test" target
 185     (inputs
 186      `(("libXt" ,libxt)
 187        ("xorgproto" ,xorgproto)
 188        ("libX11" ,libx11)
 189        ("libxml2" ,libxml2)
 190        ("mesa" ,mesa)
 191        ("glu" ,glu)
 192        ("expat" ,expat)
 193        ("freetype" ,freetype)
 194        ("hdf5" ,hdf5)
 195        ("jpeg" ,libjpeg)
 196        ("jsoncpp" ,jsoncpp)
 197        ("libogg" ,libogg)
 198        ("libtheora" ,libtheora)
 199        ("png" ,libpng)
 200        ("tiff" ,libtiff)
 201        ("zlib" ,zlib)))
 202     (home-page "https://vtk.org/")
 203     (synopsis "Libraries for 3D computer graphics")
 204     (description
 205      "The Visualization Toolkit (VTK) is a C++ library for 3D computer graphics,
 206 image processing and visualization.  It supports a wide variety of
 207 visualization algorithms including: scalar, vector, tensor, texture, and
 208 volumetric methods; and advanced modeling techniques such as: implicit
 209 modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay
 210 triangulation.  VTK has an extensive information visualization framework, has
 211 a suite of 3D interaction widgets, supports parallel processing, and
 212 integrates with various databases on GUI toolkits such as Qt and Tk.")
 213     (license license:bsd-3)))
 214
 215 (define-public opencv
 216   (package
 217     (name "opencv")
 218     (version "3.4.3")
 219     (source (origin
 220               (method git-fetch)
 221               (uri (git-reference
 222                      (url "https://github.com/opencv/opencv")
 223                      (commit version)))
 224               (file-name (git-file-name name version))
 225               (sha256
 226                (base32
 227                 "06bc61r8myym4s8im10brdjfg4wxkrvsbhhl7vr1msdan2xddzi3"))
 228               (modules '((guix build utils)))
 229               (snippet
 230                '(begin
 231                   ;; Remove external libraries. We have all available in Guix:
 232                   (delete-file-recursively "3rdparty")
 233
 234                   ;; Milky icon set is non-free:
 235                   (delete-file-recursively "modules/highgui/src/files_Qt/Milky")
 236
 237                   ;; Some jars found:
 238                   (for-each delete-file
 239                             '("modules/java/test/pure_test/lib/junit-4.11.jar"
 240                               "samples/java/sbt/sbt/sbt-launch.jar"))
 241                   #t))))
 242     (build-system cmake-build-system)
 243     (arguments
 244      `(#:configure-flags
 245        (list "-DWITH_IPP=OFF"
 246              "-DWITH_ITT=OFF"
 247              "-DWITH_CAROTENE=OFF" ; only visible on arm/aarch64
 248              "-DENABLE_PRECOMPILED_HEADERS=OFF"
 249
 250              ;; CPU-Features:
 251              ;; See cmake/OpenCVCompilerOptimizations.cmake
 252              ;; (CPU_ALL_OPTIMIZATIONS) for a list of all optimizations
 253              ;; BASELINE is the minimum optimization all CPUs must support
 254              ;;
 255              ;; DISPATCH is the list of optional dispatches.
 256              "-DCPU_BASELINE=SSE2"
 257
 258              ,@(match (%current-system)
 259                  ("x86_64-linux"
 260                   '("-DCPU_DISPATCH=NEON;VFPV3;FP16;SSE;SSE2;SSE3;SSSE3;SSE4_1;SSE4_2;POPCNT;AVX;FP16;AVX2;FMA3;AVX_512F;AVX512_SKX"
 261                     "-DCPU_DISPATCH_REQUIRE=SSE3,SSSE3,SSE4_1,SSE4_2,AVX,AVX2"))
 262                  ("armhf-linux"
 263                   '("-DCPU_BASELINE_DISABLE=NEON")) ; causes build failures
 264                  ("aarch64-linux"
 265                   '("-DCPU_BASELINE=NEON"
 266                     "-DCPU_DISPATCH=NEON;VFPV3;FP16"))
 267                  (_ '()))
 268
 269              "-DBUILD_PERF_TESTS=OFF"
 270              "-DBUILD_TESTS=ON"
 271
 272              (string-append "-DOPENCV_EXTRA_MODULES_PATH=" (getcwd)
 273                             "/opencv-contrib/modules")
 274
 275              ;;Define test data:
 276              (string-append "-DOPENCV_TEST_DATA_PATH=" (getcwd)
 277                             "/opencv-extra/testdata")
 278
 279              ;; Is ON by default and would try to rebuild 3rd-party protobuf,
 280              ;; which we had removed, which would lead to an error:
 281              "-DBUILD_PROTOBUF=OFF"
 282
 283              ;; Rebuild protobuf files, because we have a slightly different
 284              ;; version than the included one. If we would not update, we
 285              ;; would get a compile error later:
 286              "-DPROTOBUF_UPDATE_FILES=ON"
 287
 288              ;; xfeatures2d disabled, because it downloads extra binaries from
 289              ;; https://github.com/opencv/opencv_3rdparty
 290              ;; defined in xfeatures2d/cmake/download_{vgg|bootdesc}.cmake
 291              ;; Cmp this bug entry:
 292              ;; https://github.com/opencv/opencv_contrib/issues/1131
 293              "-DBUILD_opencv_xfeatures2d=OFF")
 294        #:phases
 295        (modify-phases %standard-phases
 296          (add-after 'unpack 'disable-broken-tests
 297            (lambda _
 298              ;; These tests fails with:
 299              ;; vtkXOpenGLRenderWindow (0x723990): Could not find a decent config
 300              ;; I think we have no OpenGL support with the Xvfb.
 301              (substitute* '("modules/viz/test/test_tutorial3.cpp"
 302                             "modules/viz/test/test_main.cpp"
 303                             "modules/viz/test/tests_simple.cpp"
 304                             "modules/viz/test/test_viz3d.cpp")
 305                (("(TEST\\(Viz, )([a-z].*\\).*)" all pre post)
 306                 (string-append pre "DISABLED_" post)))
 307
 308              ;; This one fails with "unknown file: Failure"
 309              ;; But I couldn't figure out which file was missing:
 310              (substitute* "../opencv-contrib/modules/face/test/test_face_align.cpp"
 311                (("(TEST\\(CV_Face_FacemarkKazemi, )(can_detect_landmarks\\).*)"
 312                  all pre post)
 313                 (string-append pre "DISABLED_" post)))
 314
 315              ;; Failure reason: Bad accuracy
 316              ;; Incorrect count of accurate poses [2nd case]: 90.000000 / 94.000000
 317              (substitute* "../opencv-contrib/modules/rgbd/test/test_odometry.cpp"
 318                (("(TEST\\(RGBD_Odometry_Rgbd, )(algorithmic\\).*)" all pre post)
 319                 (string-append pre "DISABLED_" post)))
 320              #t))
 321
 322          (add-after 'unpack 'unpack-submodule-sources
 323            (lambda* (#:key inputs #:allow-other-keys)
 324              (mkdir "../opencv-extra")
 325              (mkdir "../opencv-contrib")
 326              (copy-recursively (assoc-ref inputs "opencv-extra")
 327                                "../opencv-extra")
 328              (invoke "tar" "xvf"
 329                      (assoc-ref inputs "opencv-contrib")
 330                      "--strip-components=1"
 331                      "-C" "../opencv-contrib")))
 332
 333          (add-after 'set-paths 'add-ilmbase-include-path
 334            (lambda* (#:key inputs #:allow-other-keys)
 335            ;; OpenEXR propagates ilmbase, but its include files do not appear
 336            ;; in the CPATH, so we need to add "$ilmbase/include/OpenEXR/" to
 337            ;; the CPATH to satisfy the dependency on "ImathVec.h".
 338            (setenv "CPATH"
 339                    (string-append (assoc-ref inputs "ilmbase")
 340                                   "/include/OpenEXR"
 341                                   ":" (or (getenv "CPATH") "")))
 342            #t))
 343        (add-before 'check 'start-xserver
 344          (lambda* (#:key inputs #:allow-other-keys)
 345            (let ((xorg-server (assoc-ref inputs "xorg-server"))
 346                  (disp ":1"))
 347              (setenv "HOME" (getcwd))
 348              (setenv "DISPLAY" disp)
 349              ;; There must be a running X server and make check doesn't start one.
 350              ;; Therefore we must do it.
 351              (zero? (system (format #f "~a/bin/Xvfb ~a &" xorg-server disp)))))))))
 352     (native-inputs
 353      `(("pkg-config" ,pkg-config)
 354        ("xorg-server" ,xorg-server) ; For running the tests
 355        ("opencv-extra"
 356         ,(origin
 357            (method git-fetch)
 358            (uri (git-reference
 359                   (url "https://github.com/opencv/opencv_extra")
 360                   (commit version)))
 361            (file-name (git-file-name "opencv_extra" version))
 362            (sha256
 363             (base32 "08p5xnq8n1jw8svvz0fnirfg7q8dm3p4a5dl7527s5xj0f9qn7lp"))))
 364        ("opencv-contrib"
 365         ,(origin
 366            (method git-fetch)
 367            (uri (git-reference
 368                   (url "https://github.com/opencv/opencv_contrib")
 369                   (commit version)))
 370            (file-name (git-file-name "opencv_contrib" version))
 371            (patches (search-patches "opencv-rgbd-aarch64-test-fix.patch"))
 372            (sha256
 373             (base32 "1f334glf39nk42mpqq6j732h3ql2mpz89jd4mcl678s8n73nfjh2"))))))
 374     (inputs `(("libjpeg" ,libjpeg)
 375               ("libpng" ,libpng)
 376               ("jasper" ,jasper)
 377               ;; ffmpeg 4.0 causes core dumps in tests.
 378               ("ffmpeg" ,ffmpeg-3.4)
 379               ("libtiff" ,libtiff)
 380               ("hdf5" ,hdf5)
 381               ("libgphoto2" ,libgphoto2)
 382               ("libwebp" ,libwebp)
 383               ("zlib" ,zlib)
 384               ("gtkglext" ,gtkglext)
 385               ("openexr" ,openexr)
 386               ("ilmbase" ,ilmbase)
 387               ("gtk+" ,gtk+-2)
 388               ("python-numpy" ,python-numpy)
 389               ("protobuf" ,protobuf)
 390               ("vtk" ,vtk)
 391               ("python" ,python)))
 392     ;; These three CVEs are not a problem of OpenCV, see:
 393     ;; https://github.com/opencv/opencv/issues/10998
 394     (properties '((lint-hidden-cve . ("CVE-2018-7712"
 395                                       "CVE-2018-7713"
 396                                       "CVE-2018-7714"))))
 397     (synopsis "Computer vision library")
 398     (description "OpenCV is a library aimed at
 399 real-time computer vision, including several hundred computer
 400 vision algorithms.  It can be used to do things like:
 401
 402 @itemize
 403 @item image and video input and output
 404 @item image and video processing
 405 @item displaying
 406 @item feature recognition
 407 @item segmentation
 408 @item facial recognition
 409 @item stereo vision
 410 @item structure from motion
 411 @item augmented reality
 412 @item machine learning
 413 @end itemize\n")
 414     (home-page "https://opencv.org/")
 415     (license license:bsd-3)))
 416
 417 (define-public vips
 418   (package
 419     (name "vips")
 420     (version "8.7.4")
 421     (source
 422      (origin
 423        (method url-fetch)
 424        (uri (string-append
 425              "https://github.com/libvips/libvips/releases/download/v"
 426              version "/vips-" version ".tar.gz"))
 427        (sha256
 428         (base32 "01gjhcrl6zj7mcj1al717v5jsniahplqhz1xkfh2j78vyfl1hxff"))))
 429     (build-system gnu-build-system)
 430     (native-inputs
 431      `(("pkg-config" ,pkg-config)
 432        ("gobject-introspection" ,gobject-introspection)))
 433     (inputs
 434      `(("glib" ,glib)
 435        ("libjpeg" ,libjpeg)
 436        ("libpng" ,libpng)
 437        ("librsvg" ,librsvg)
 438        ("libtiff" ,libtiff)
 439        ("libexif" ,libexif)
 440        ("giflib" ,giflib)
 441        ("libgsf" ,libgsf)
 442        ("fftw" ,fftw)
 443        ("poppler" ,poppler)
 444        ("pango" ,pango)
 445        ("lcms" ,lcms)
 446        ("matio" ,matio)
 447        ("libwebp" ,libwebp)
 448        ("niftilib" ,niftilib)
 449        ("openexr" ,openexr)
 450        ("orc" ,orc)
 451        ("imagemagick" ,imagemagick)
 452        ("libxml2" ,libxml2)
 453        ("expat" ,expat)
 454        ("hdf5" ,hdf5)))
 455     (home-page "https://libvips.github.io/libvips/")
 456     (synopsis "Multithreaded image processing system with low memory needs")
 457     (description
 458      "VIPS is a demand-driven, horizontally threaded image processing library.
 459 It's particularly good at processing large images, working with colour,
 460 scientific analysis, and general research & development.
 461
 462 Compared to most image processing libraries VIPS needs little RAM and runs
 463 quickly, especially on machines with more than one CPU core.  This is primarily
 464 due to its architecture which automatically parallelises the image workflows.")
 465     (license license:lgpl2.1+)))
 466
 467 (define-public nip2
 468   (package
 469     (name "nip2")
 470     (version "8.7.1")
 471     (source
 472      (origin
 473        (method url-fetch)
 474        (uri (string-append "https://github.com/libvips/nip2/releases/download/v"
 475                            version "/nip2-" version ".tar.gz" ))
 476        (sha256
 477         (base32 "0l7n427njif53npqn02gfjjly8y3khbrkzqxp10j5vp9h97psgiw"))))
 478     (build-system gnu-build-system)
 479     (arguments
 480      `(#:phases
 481        (modify-phases %standard-phases
 482          ;; test_conv.ws keep failing so disabling for now.
 483          (add-after 'unpack 'disable-test-conv
 484            (lambda _
 485              (delete-file "test/workspaces/test_conv.ws")
 486              #t))
 487          (add-before 'check 'set-home
 488            (lambda _
 489              (setenv "HOME" "/tmp") #t)))))
 490     (inputs
 491      `(("vips" ,vips)
 492        ("glib" ,glib)
 493        ("libtiff" ,libtiff)
 494        ("gtk+-2" ,gtk+-2)
 495        ("libxml2" ,libxml2)
 496        ("libexif" ,libexif)
 497        ("libjpeg" ,libjpeg)             ; required by vips.pc
 498        ("librsvg" ,librsvg)
 499        ("fftw" ,fftw)
 500        ("libgsf" ,libgsf)
 501        ("imagemagick" ,imagemagick)
 502        ("orc" ,orc)
 503        ("matio" ,matio)
 504        ("lcms" ,lcms)
 505        ("libwebp" ,libwebp)
 506        ("openexr" ,openexr)
 507        ("poppler" ,poppler)
 508        ("gsl" ,gsl)))
 509     (native-inputs
 510      `(("flex" ,flex)
 511        ("bison" ,bison)
 512        ("pkg-config" ,pkg-config)))
 513     (home-page "https://github.com/libvips/nip2")
 514     (synopsis "Spreadsheet-like GUI for libvips")
 515     (description "This package provide a graphical user interface (GUI) for
 516 the VIPS image processing library.  It's a little like a spreadsheet: you
 517 create a set of formula connecting your objects together, and on a change nip2
 518 recalculates.")
 519     (license license:gpl2+)))