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