gnu/packages/image-processing.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2017 John Darrington <jmd@gnu.org>
   3 ;;; Copyright © 2017, 2019, 2022 Ricardo Wurmus <rekado@elephly.net>
   4 ;;; Copyright © 2014, 2021-2022 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 © 2018–2021 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, 2021 Efraim Flashner <efraim@flashner.co.il>
  11 ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
  12 ;;; Copyright © 2020, 2021 Vinicius Monego <monego@posteo.net>
  13 ;;; Copyright © 2020 Pierre Neidhardt <mail@ambrevar.xyz>
  14 ;;; Copyright © 2020 Brendan Tildesley <mail@brendan.scot>
  15 ;;; Copyright © 2021 Oleh Malyi <astroclubzp@gmail.com>
  16 ;;; Copyright © 2021, 2022 Felix Gruber <felgru@posteo.net>
  17 ;;; Copyright © 2021 Andy Tai <atai@atai.org>
  18 ;;; Copyright © 2021 Ekaitz Zarraga <ekaitz@elenq.tech>
  19 ;;; Copyright © 2021 Paul Garlick <pgarlick@tourbillion-technology.com>
  20 ;;; Copyright © 2021 Guillaume Le Vaillant <glv@posteo.net>
  21 ;;; Copyright © 2021 Ivan Gankevich <i.gankevich@spbu.ru>
  22 ;;; Copyright © 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
  23 ;;; Copyright © 2022 Tomasz Jeneralczyk <tj@schwi.pl>
  24 ;;;
  25 ;;; This file is part of GNU Guix.
  26 ;;;
  27 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  28 ;;; under the terms of the GNU General Public License as published by
  29 ;;; the Free Software Foundation; either version 3 of the License, or (at
  30 ;;; your option) any later version.
  31 ;;;
  32 ;;; GNU Guix is distributed in the hope that it will be useful, but
  33 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  34 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  35 ;;; GNU General Public License for more details.
  36 ;;;
  37 ;;; You should have received a copy of the GNU General Public License
  38 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  39
  40 (define-module (gnu packages image-processing)
  41   #:use-module ((guix licenses) #:prefix license:)
  42   #:use-module (guix packages)
  43   #:use-module (guix gexp)
  44   #:use-module (guix utils)
  45   #:use-module (guix download)
  46   #:use-module (guix git-download)
  47   #:use-module (guix build-system qt)
  48   #:use-module (guix build-system cmake)
  49   #:use-module (guix build-system gnu)
  50   #:use-module (guix build-system python)
  51   #:use-module (gnu packages)
  52   #:use-module (gnu packages algebra)
  53   #:use-module (gnu packages bison)
  54   #:use-module (gnu packages boost)
  55   #:use-module (gnu packages check)
  56   #:use-module (gnu packages compression)
  57   #:use-module (gnu packages curl)
  58   #:use-module (gnu packages docbook)
  59   #:use-module (gnu packages documentation)
  60   #:use-module (gnu packages flex)
  61   #:use-module (gnu packages fontutils)
  62   #:use-module (gnu packages geo)
  63   #:use-module (gnu packages ghostscript)
  64   #:use-module (gnu packages gimp)
  65   #:use-module (gnu packages gl)
  66   #:use-module (gnu packages glib)
  67   #:use-module (gnu packages gnome)
  68   #:use-module (gnu packages graphics)
  69   #:use-module (gnu packages graphviz)
  70   #:use-module (gnu packages gstreamer)
  71   #:use-module (gnu packages gtk)
  72   #:use-module (gnu packages icu4c)
  73   #:use-module (gnu packages image)
  74   #:use-module (gnu packages imagemagick)
  75   #:use-module (gnu packages linux)
  76   #:use-module (gnu packages maths)
  77   #:use-module (gnu packages pdf)
  78   #:use-module (gnu packages perl)
  79   #:use-module (gnu packages photo)
  80   #:use-module (gnu packages pkg-config)
  81   #:use-module (gnu packages protobuf)
  82   #:use-module (gnu packages python)
  83   #:use-module (gnu packages python-check)
  84   #:use-module (gnu packages python-xyz)
  85   #:use-module (gnu packages qt)
  86   #:use-module (gnu packages serialization)
  87   #:use-module (gnu packages sqlite)
  88   #:use-module (gnu packages tbb)
  89   #:use-module (gnu packages tls)
  90   #:use-module (gnu packages version-control)
  91   #:use-module (gnu packages video)
  92   #:use-module (gnu packages xiph)
  93   #:use-module (gnu packages xml)
  94   #:use-module (gnu packages xorg)
  95   #:use-module (ice-9 match)
  96   #:use-module (srfi srfi-1))
  97
  98 ;; TODO: this is not reproducible.
  99 (define-public bart
 100   (package
 101     (name "bart")
 102     (version "0.7.00")
 103     (source
 104      (origin
 105        (method git-fetch)
 106        (uri (git-reference
 107              (url "https://github.com/mrirecon/bart")
 108              (commit "d1b0e576c3f759089915565d5bf57832acf7b03e")))
 109        (file-name (git-file-name name version))
 110        (sha256
 111         (base32 "159rj3agr9pb9lg38b56rnw3d8wcbkmb2n718z26zpy4c6a6d9rn"))))
 112     (build-system gnu-build-system)
 113     (arguments
 114      (list
 115       #:test-target "utest"
 116       #:make-flags #~(list
 117                       (string-append "PREFIX=" #$output)
 118                       "OPENBLAS=1"
 119                       "SCALAPACK=1"
 120                       (string-append "BLAS_BASE=" #$(this-package-input "openblas"))
 121                       (string-append "FFTW_BASE=" #$(this-package-input "fftw")))
 122       #:phases
 123       #~(modify-phases %standard-phases
 124           (delete 'configure)
 125           (add-after 'unpack 'patch-/bin/bash
 126             (lambda _
 127               (substitute* "tests/pics.mk"
 128                 (("/bin/bash") (which "bash"))))))))
 129     (inputs
 130      (list fftw
 131            fftwf
 132            libpng
 133            openblas
 134            python
 135            scalapack))
 136     (native-inputs
 137      (list doxygen
 138            util-linux)) ;for flock
 139     (home-page "https://mrirecon.github.io/bart/")
 140     (synopsis "Toolbox for computational magnetic resonance imaging")
 141     (description "The Berkeley Advanced Reconstruction Toolbox (BART) is an
 142 image-reconstruction framework for Computational Magnetic Resonance Imaging.
 143 The tools in this software implement various reconstruction algorithms for
 144 Magnetic Resonance Imaging.")
 145     (license license:bsd-3)))
 146
 147 (define-public dcmtk
 148   (package
 149     (name "dcmtk")
 150     (version "3.6.7")
 151     (source
 152      (origin
 153        (method url-fetch)
 154        (uri
 155         (string-append "ftp://dicom.offis.de/pub/dicom/offis/software/dcmtk/"
 156                        "dcmtk" (string-join (string-split version #\.) "")
 157                        "/dcmtk-" version ".tar.gz"))
 158        (sha256
 159         (base32 "02kix73qhndgb56cmi5327666i6imp7hi17wwqp26q4d7s72jn3w"))))
 160     (build-system cmake-build-system)
 161     (arguments
 162      ;; By default, only static archives are built.
 163      (list #:configure-flags #~(list "-DBUILD_SHARED_LIBS=ON")))
 164     (inputs
 165      (list icu4c
 166            libjpeg-turbo
 167            libpng
 168            libtiff
 169            libxml2
 170            openssl
 171            zlib))
 172     (native-inputs
 173      (list doxygen))           ; for HTML documentation
 174     (home-page "https://dcmtk.org")
 175     (synopsis "Libraries and programs implementing parts of the DICOM standard")
 176     (description "DCMTK is a collection of libraries and applications
 177 implementing large parts the DICOM standard.  It includes software for
 178 examining, constructing and converting DICOM image files, handling offline
 179 media, sending and receiving images over a network connection, as well as
 180 demonstrative image storage and worklist servers.")
 181     (license (license:fsf-free
 182               "file://COPYRIGHT"
 183               "A union of the Apache 2.0 licence and various non-copyleft
 184 licences similar to the Modified BSD licence."))))
 185
 186 (define-public mia
 187   (package
 188     (name "mia")
 189     (version "2.4.7")
 190     (source (origin
 191               (method url-fetch)
 192               (uri (string-append "mirror://sourceforge/mia/mia/"
 193                                   (version-major+minor version)
 194                                   "/mia-" version ".tar.xz"))
 195               (sha256
 196                (base32
 197                 "0qpcd3n26q52dpyibm11f5l6cgscdr54p2jish39gc3p1f5h3ws1"))
 198               (patches (search-patches "mia-fix-boost-headers.patch"
 199                                        "mia-vtk9.patch"))))
 200     (build-system cmake-build-system)
 201     (arguments
 202      `(#:configure-flags
 203        (list "-DMIA_CREATE_NIPYPE_INTERFACES=OFF"
 204              "-DCMAKE_CXX_FLAGS=-fpermissive")))
 205     (inputs
 206      (list boost
 207            dcmtk
 208            doxygen
 209            eigen
 210            fftw
 211            fftwf
 212            gsl
 213            gts
 214            hdf5
 215            itpp
 216            libjpeg-turbo
 217            libpng
 218            libtiff
 219            libxml2
 220            libxml++
 221            maxflow
 222            niftilib
 223            nlopt
 224            openexr-2
 225            python-lxml
 226            vtk))
 227     (native-inputs
 228      (list pkg-config
 229            python-wrapper))
 230     (home-page "http://mia.sourceforge.net")
 231     (synopsis "Toolkit for gray scale medical image analysis")
 232     (description "MIA provides a combination of command line tools, plug-ins,
 233 and libraries that make it possible run image processing tasks interactively
 234 in a command shell and to prototype using the shell's scripting language.  It
 235 is built around a plug-in structure that makes it easy to add functionality
 236 without compromising the original code base and it makes use of a wide variety
 237 of external libraries that provide additional functionality.")
 238     (license license:gpl3+)))
 239
 240 (define-public opencolorio
 241   (package
 242     (name "opencolorio")
 243     (version "1.1.1")
 244     (source
 245      (origin
 246        (method git-fetch)
 247        (uri (git-reference
 248              (url "https://github.com/AcademySoftwareFoundation/OpenColorIO")
 249              (commit (string-append "v" version))))
 250        (sha256
 251         (base32 "12srvxca51czpfjl0gabpidj9n84mw78ivxy5w75qhq2mmc798sb"))
 252        (file-name (git-file-name name version))
 253        (modules '((guix build utils)))
 254        (snippet
 255         `(begin
 256            ;; Remove bundled tarballs, patches, and .jars(!).  XXX: Upstream
 257            ;; claims to have fixed USE_EXTERNAL_YAML, but it still fails with:
 258            ;; https://github.com/AcademySoftwareFoundation/OpenColorIO/issues/517
 259            ;; When removing it, also remove it from the licence field comment.
 260            (for-each delete-file-recursively
 261                      (filter
 262                       (lambda (full-name)
 263                         (let ((file (basename full-name)))
 264                           (not (or (string-prefix? "yaml-cpp-0.3" file)
 265                                    (string=? "unittest.h" file)))))
 266                       (find-files "ext" ".*")))
 267
 268            #t))))
 269     (build-system cmake-build-system)
 270     (arguments
 271      `(#:configure-flags
 272        (list (string-append "-DCMAKE_CXX_FLAGS="
 273                             "-Wno-error=deprecated-declarations "
 274                             "-Wno-error=unused-function")
 275              "-DOCIO_BUILD_STATIC=OFF"
 276              ;; "-DUSE_EXTERNAL_YAML=ON"
 277              "-DUSE_EXTERNAL_TINYXML=ON"
 278              "-DUSE_EXTERNAL_LCMS=ON")
 279        #:phases
 280        (modify-phases %standard-phases
 281          (add-after 'unpack 'patch-test-suite
 282            (lambda _
 283              (substitute* "src/core_tests/CMakeLists.txt"
 284                (("/bin/sh") (which "bash")))
 285              #t)))))
 286     (native-inputs
 287      (list git pkg-config))
 288     (inputs
 289      ;; XXX Adding freeglut, glew, ilmbase, mesa, and openimageio for
 290      ;; ocioconvert fails: error: conflicting declaration ?typedef void
 291      ;; (* PFNGLGETFRAGMENTMATERIALFVSGIXPROC)(GLenum, GLenum, GLfloat*)
 292      (list lcms openexr-2 tinyxml))
 293     (home-page "https://opencolorio.org")
 294     (synopsis "Color management for visual effects and animation")
 295     (description
 296      "OpenColorIO, or OCIO, is a complete color management solution geared
 297 towards motion picture production, with an emphasis on visual effects and
 298 computer animation.  It provides a straightforward and consistent user
 299 experience across all supporting applications while allowing for sophisticated
 300 back-end configuration options suitable for high-end production usage.
 301
 302 OCIO is compatible with the @acronym{ACES, Academy Color Encoding
 303 Specification} and is @acronym{LUT, look-up table}-format agnostic, supporting
 304 many popular formats.")
 305     (license (list license:expat        ; docs/ociotheme/static, ext/yaml-cpp-*
 306                    license:zlib         ; src/core/md5
 307                    license:bsd-3))))    ; the rest
 308
 309 (define-public vtk
 310   (package
 311     (name "vtk")
 312     (version "9.0.1")
 313     (source (origin
 314               (method url-fetch)
 315               (uri (string-append "https://vtk.org/files/release/"
 316                                   (version-major+minor version)
 317                                   "/VTK-" version ".tar.gz"))
 318               (sha256
 319                (base32
 320                 "1ir2lq9i45ls374lcmjzw0nrm5l5hnm1w47lg8g8d0n2j7hsaf8v"))
 321               (patches
 322                (search-patches "vtk-fix-freetypetools-build-failure.patch"))
 323               (modules '((guix build utils)))
 324               (snippet
 325                '(begin
 326                   (for-each
 327                    (lambda (dir)
 328                      (delete-file-recursively
 329                       (string-append "ThirdParty/" dir "/vtk" dir)))
 330                    ;; pugixml depended upon unconditionally
 331                    '("doubleconversion" "eigen" "expat" "freetype" "gl2ps"
 332                      "glew" "hdf5" "jpeg" "jsoncpp" "libharu" "libproj"
 333                      "libxml2" "lz4" "netcdf" "ogg" "png" "sqlite" "theora"
 334                      "tiff" "zlib"))
 335                   (substitute* "IO/ExportPDF/vtkPDFContextDevice2D.cxx"
 336                     (("\\bHPDF_UINT16 (noPen|dash|dot|denseDot|dashDot|dashDotDot)\\b"
 337                       _ var)
 338                      (string-append "HPDF_REAL " var)))))))
 339     (properties `((release-monitoring-url . "https://vtk.org/download/")))
 340     (build-system cmake-build-system)
 341     (arguments
 342      '(#:build-type "Release"           ;Build without '-g' to save space.
 343        #:configure-flags '(;"-DBUILD_TESTING:BOOL=TRUE"
 344                            ;    ; not honored
 345                            "-DVTK_USE_EXTERNAL=OFF" ;; default
 346                            "-DVTK_MODULE_USE_EXTERNAL_VTK_doubleconversion=ON"
 347                            "-DVTK_MODULE_USE_EXTERNAL_VTK_eigen=ON"
 348                            "-DVTK_MODULE_USE_EXTERNAL_VTK_expat=ON"
 349                            "-DVTK_MODULE_USE_EXTERNAL_VTK_freetype=ON"
 350                            "-DVTK_MODULE_USE_EXTERNAL_VTK_gl2ps=ON"
 351                            "-DVTK_MODULE_USE_EXTERNAL_VTK_glew=ON"
 352                            "-DVTK_MODULE_USE_EXTERNAL_VTK_hdf5=ON"
 353                            "-DVTK_MODULE_USE_EXTERNAL_VTK_jpeg=ON"
 354                            "-DVTK_MODULE_USE_EXTERNAL_VTK_jsoncpp=ON"
 355                            "-DVTK_MODULE_USE_EXTERNAL_VTK_libharu=ON"
 356                            "-DVTK_MODULE_USE_EXTERNAL_VTK_libproj=ON"
 357                            "-DVTK_MODULE_USE_EXTERNAL_VTK_libxml2=ON"
 358                            "-DVTK_MODULE_USE_EXTERNAL_VTK_lz4=ON"
 359                            "-DVTK_MODULE_USE_EXTERNAL_VTK_netcdf=ON"
 360                            "-DVTK_MODULE_USE_EXTERNAL_VTK_ogg=ON"
 361                            "-DVTK_MODULE_USE_EXTERNAL_VTK_png=ON"
 362                            ;"-DVTK_MODULE_USE_EXTERNAL_VTK_pugixml=ON"    ; breaks IO/CityGML
 363                            "-DVTK_MODULE_USE_EXTERNAL_VTK_sqlite=ON"
 364                            "-DVTK_MODULE_USE_EXTERNAL_VTK_theora=ON"
 365                            "-DVTK_MODULE_USE_EXTERNAL_VTK_tiff=ON"
 366                            "-DVTK_MODULE_USE_EXTERNAL_VTK_zlib=ON"
 367                            "-DVTK_MODULE_ENABLE_VTK_RenderingExternal=YES" ; For F3D
 368                            "-DVTK_WRAP_PYTHON=ON"
 369                            "-DVTK_PYTHON_VERSION:STRING=3"
 370                            )
 371        #:phases
 372          (modify-phases %standard-phases
 373            (add-after 'unpack 'patch-sources
 374              (lambda _
 375                (substitute* "Common/Core/vtkFloatingPointExceptions.cxx"
 376                  (("<fenv.h>") "<cfenv>"))
 377                (substitute* "Common/Core/CMakeLists.txt"
 378                  (("fenv.h") "cfenv")))))
 379        #:tests? #f))        ;XXX: test data not included
 380     (inputs
 381      (list double-conversion
 382            eigen
 383            expat
 384            freetype
 385            gl2ps
 386            glew
 387            glu
 388            hdf5
 389            libharu
 390            libjpeg-turbo
 391            jsoncpp
 392            libtheora
 393            libx11
 394            libxml2
 395            libxt
 396            lz4
 397            mesa
 398            netcdf
 399            libpng
 400            proj-7
 401            python
 402            ;("pugixml" ,pugixml)
 403            sqlite
 404            libtiff
 405            xorgproto
 406            zlib))
 407     (propagated-inputs
 408      ;; VTK's 'VTK-vtk-module-find-packages.cmake' calls
 409      ;; 'find_package(THEORA)', which in turns looks for libogg.
 410      (list libogg))
 411     (home-page "https://vtk.org/")
 412     (synopsis "Libraries for 3D computer graphics")
 413     (description
 414      "The Visualization Toolkit (VTK) is a C++ library for 3D computer graphics,
 415 image processing and visualization.  It supports a wide variety of
 416 visualization algorithms including: scalar, vector, tensor, texture, and
 417 volumetric methods; and advanced modeling techniques such as: implicit
 418 modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay
 419 triangulation.  VTK has an extensive information visualization framework, has
 420 a suite of 3D interaction widgets, supports parallel processing, and
 421 integrates with various databases on GUI toolkits such as Qt and Tk.")
 422     (license license:bsd-3)))
 423
 424 (define-public vtk-7
 425   (package
 426     (inherit vtk)
 427     (version "7.1.1")
 428     (source (origin
 429               (method url-fetch)
 430               (uri (string-append "https://vtk.org/files/release/"
 431                                   (version-major+minor version)
 432                                   "/VTK-" version ".tar.gz"))
 433               (sha256
 434                (base32
 435                 "0nm7xwwj7rnsxjdv2ssviys8nhci4n9iiiqm2y14s520hl2dsp1d"))
 436               (patches (search-patches "vtk-7-python-compat.patch"
 437                                        "vtk-7-hdf5-compat.patch"
 438                                        "vtk-7-gcc-10-compat.patch"))))
 439     (arguments
 440      (substitute-keyword-arguments (package-arguments vtk)
 441        ((#:configure-flags flags)
 442         ;; Otherwise, the build would fail with: "error: invalid conversion
 443         ;; from ‘const char*’ to ‘char*’ [-fpermissive]".
 444         `(cons "-DCMAKE_CXX_FLAGS=-fpermissive" ,flags))
 445        ((#:phases phases)
 446         #~(modify-phases #$phases
 447             (add-after 'unpack 'remove-kernel-version
 448               ;; Avoid embedding the kernel version for reproducible builds
 449               (lambda _
 450                 (substitute*
 451                     "ThirdParty/hdf5/vtkhdf5/config/cmake/libhdf5.settings.cmake.in"
 452                   (("Host system: \\@CMAKE_HOST_SYSTEM\\@")
 453                    "Host system: @CMAKE_SYSTEM_NAME@"))))))))))
 454
 455 (define-public opencv
 456   (package
 457     (name "opencv")
 458     (version "4.5.4")
 459     (source (origin
 460               (method git-fetch)
 461               (uri (git-reference
 462                      (url "https://github.com/opencv/opencv")
 463                      (commit version)))
 464               (file-name (git-file-name name version))
 465               (sha256
 466                (base32
 467                 "0gf2xs3r4s51m20mpf0wdidpk0xzp3m2w6jx72fwldhn0pshlmcj"))
 468               (modules '((guix build utils)))
 469               (snippet
 470                '(begin
 471                   ;; Remove external libraries. We have almost all available
 472                   ;; in Guix:
 473                   (with-directory-excursion "3rdparty"
 474                     (for-each delete-file-recursively
 475                               '("carotene"
 476                                 "cpufeatures"
 477                                 "ffmpeg"
 478                                 "include"
 479                                 "ippicv"
 480                                 "ittnotify"
 481                                 "libjasper"
 482                                 "libjpeg"
 483                                 "libjpeg-turbo"
 484                                 "libpng"
 485                                 "libtengine"
 486                                 "libtiff"
 487                                 "libwebp"
 488                                 "openexr"
 489                                 "openjpeg"
 490                                 "openvx"
 491                                 "protobuf"
 492                                 ;;"quirc"
 493                                 "tbb"
 494                                 "zlib")))
 495
 496                   ;; Milky icon set is non-free:
 497                   (delete-file-recursively "modules/highgui/src/files_Qt/Milky")
 498
 499                   ;; Some jars found:
 500                   (for-each delete-file
 501                             '("modules/java/test/pure_test/lib/junit-4.11.jar"
 502                               "samples/java/sbt/sbt/sbt-launch.jar"))))))
 503     (build-system cmake-build-system)
 504     (arguments
 505      `(#:configure-flags
 506        (list "-DWITH_ADE=OFF" ;we don't have a package for ade yet
 507              "-DWITH_IPP=OFF"
 508              "-DWITH_ITT=OFF"
 509              "-DWITH_CAROTENE=OFF" ; only visible on arm/aarch64
 510              "-DENABLE_PRECOMPILED_HEADERS=OFF"
 511              "-DOPENCV_GENERATE_PKGCONFIG=ON"
 512
 513              ;; CPU-Features:
 514              ;; See cmake/OpenCVCompilerOptimizations.cmake
 515              ;; (CPU_ALL_OPTIMIZATIONS) for a list of all optimizations
 516              ;; BASELINE is the minimum optimization all CPUs must support
 517              ;;
 518              ;; DISPATCH is the list of optional dispatches.
 519              "-DCPU_BASELINE=SSE2"
 520
 521              ;; Build Python bindings.
 522              "-DBUILD_opencv_python3=ON"
 523
 524              ,@(match (%current-system)
 525                  ("x86_64-linux"
 526                   '("-DCPU_DISPATCH=NEON;VFPV3;FP16;SSE;SSE2;SSE3;SSSE3;SSE4_1;SSE4_2;POPCNT;AVX;FP16;AVX2;FMA3;AVX_512F;AVX512_SKX"
 527                     "-DCPU_DISPATCH_REQUIRE=SSE3,SSSE3,SSE4_1,SSE4_2,AVX,AVX2"))
 528                  ("armhf-linux"
 529                   '("-DCPU_BASELINE_DISABLE=NEON")) ; causes build failures
 530                  ("aarch64-linux"
 531                   '("-DCPU_BASELINE=NEON"
 532                     "-DCPU_DISPATCH=NEON;VFPV3;FP16"))
 533                  (_ '()))
 534
 535              "-DBUILD_PERF_TESTS=OFF"
 536              "-DBUILD_TESTS=ON"
 537
 538              (string-append "-DOPENCV_EXTRA_MODULES_PATH=" (getcwd)
 539                             "/opencv-contrib/modules")
 540
 541              ;;Define test data:
 542              (string-append "-DOPENCV_TEST_DATA_PATH=" (getcwd)
 543                             "/opencv-extra/testdata")
 544
 545              ;; Is ON by default and would try to rebuild 3rd-party protobuf,
 546              ;; which we had removed, which would lead to an error:
 547              "-DBUILD_PROTOBUF=OFF"
 548
 549              ;; Rebuild protobuf files, because we have a slightly different
 550              ;; version than the included one. If we would not update, we
 551              ;; would get a compile error later:
 552              "-DPROTOBUF_UPDATE_FILES=ON"
 553
 554              ;; xfeatures2d disabled, because it downloads extra binaries from
 555              ;; https://github.com/opencv/opencv_3rdparty
 556              ;; defined in xfeatures2d/cmake/download_{vgg|bootdesc}.cmake
 557              ;; Cmp this bug entry:
 558              ;; https://github.com/opencv/opencv_contrib/issues/1131
 559              "-DBUILD_opencv_xfeatures2d=OFF")
 560        #:phases
 561        (modify-phases %standard-phases
 562          (add-after 'unpack 'disable-broken-tests
 563            (lambda _
 564              ;; This test fails with "unknown file: Failure"
 565              ;; But I couldn't figure out which file was missing:
 566              (substitute* "../opencv-contrib/modules/face/test/test_face_align.cpp"
 567                (("(TEST\\(CV_Face_FacemarkKazemi, )(can_detect_landmarks\\).*)"
 568                  all pre post)
 569                 (string-append pre "DISABLED_" post)))
 570
 571              ;; This test fails with a comparison between the expected 396 and
 572              ;; the actual 440 in file size.
 573              (substitute* "modules/imgcodecs/test/test_exr.impl.hpp"
 574                (("(TEST\\(Imgcodecs_EXR, )(readWrite_32FC1\\).*)" all pre post)
 575                 (string-append pre "DISABLED_" post)))
 576
 577              ;; These fail with protobuf parse errors that come from
 578              ;; opencv-extra/testdata.
 579              (substitute* "modules/dnn/test/test_layers.cpp"
 580                (("(TEST_P\\(Test_Caffe_layers, )\
 581 (Accum\\).*|DataAugmentation\\).*|Resample\\).*|Correlation\\).*)" all pre post)
 582                 (string-append pre "DISABLED_" post)))))
 583          (add-after 'unpack 'unpack-submodule-sources
 584            (lambda* (#:key inputs #:allow-other-keys)
 585              (mkdir "../opencv-extra")
 586              (mkdir "../opencv-contrib")
 587              (copy-recursively (assoc-ref inputs "opencv-extra")
 588                                "../opencv-extra")
 589              (copy-recursively (assoc-ref inputs "opencv-contrib")
 590                                "../opencv-contrib")))
 591          (add-after 'build 'do-not-install-3rdparty-file
 592            (lambda _
 593              (substitute* "cmake_install.cmake"
 594                (("file\\(INSTALL .*source/3rdparty/include/opencl/LICENSE.txt.*") "\n"))))
 595          (add-before 'check 'start-xserver
 596            (lambda* (#:key inputs #:allow-other-keys)
 597              (let ((xorg-server (assoc-ref inputs "xorg-server"))
 598                    (disp ":1"))
 599                (setenv "HOME" (getcwd))
 600                (setenv "DISPLAY" disp)
 601                ;; There must be a running X server and make check doesn't start one.
 602                ;; Therefore we must do it.
 603                (zero? (system (format #f "~a/bin/Xvfb ~a &" xorg-server disp)))))))))
 604     (native-inputs
 605      `(("pkg-config" ,pkg-config)
 606        ("xorg-server" ,xorg-server-for-tests) ; For running the tests
 607        ("opencv-extra"
 608         ,(origin
 609            (method git-fetch)
 610            (uri (git-reference
 611                  (url "https://github.com/opencv/opencv_extra")
 612                  (commit version)))
 613            (file-name (git-file-name "opencv_extra" version))
 614            (sha256
 615             (base32 "1fg2hxdvphdvagc2fkmhqk7qql9mp7pj2bmp8kmd7vicpr72qk82"))))
 616        ("opencv-contrib"
 617         ,(origin
 618            (method git-fetch)
 619            (uri (git-reference
 620                  (url "https://github.com/opencv/opencv_contrib")
 621                  (commit version)))
 622            (file-name (git-file-name "opencv_contrib" version))
 623            (sha256
 624             (base32 "0ga0l4ranp1834gxgp487ll1amvmssa02l2nk5ja5w0rx4d8hh26"))))))
 625     (inputs
 626      (list ffmpeg
 627            gtk+
 628            gtkglext
 629            hdf5
 630            ilmbase
 631            imath ;should be propagated by openexr
 632            jasper
 633            libgphoto2
 634            libjpeg-turbo
 635            libpng
 636            libtiff
 637            libwebp
 638            openblas
 639            openexr
 640            openjpeg
 641            protobuf
 642            python
 643            python-numpy
 644            vtk
 645            zlib))
 646     ;; These three CVEs are not a problem of OpenCV, see:
 647     ;; https://github.com/opencv/opencv/issues/10998
 648     (properties '((lint-hidden-cve . ("CVE-2018-7712"
 649                                       "CVE-2018-7713"
 650                                       "CVE-2018-7714"))))
 651     (synopsis "Computer vision library")
 652     (description "OpenCV is a library aimed at real-time computer vision,
 653 including several hundred computer vision algorithms.  It can be used to do
 654 things like:
 655
 656 @itemize
 657 @item image and video input and output
 658 @item image and video processing
 659 @item displaying
 660 @item feature recognition
 661 @item segmentation
 662 @item facial recognition
 663 @item stereo vision
 664 @item structure from motion
 665 @item augmented reality
 666 @item machine learning
 667 @end itemize\n")
 668     (home-page "https://opencv.org/")
 669     (license license:bsd-3)))
 670
 671 (define-public vips
 672   (package
 673     (name "vips")
 674     (version "8.13.1")
 675     (source
 676      (origin
 677        (method url-fetch)
 678        (uri (string-append
 679              "https://github.com/libvips/libvips/releases/download/v"
 680              version "/vips-" version ".tar.gz"))
 681        (sha256
 682         (base32 "00kp3439jcqv9l2gcjg88xzvlq8clv54z1m3x66i3chvarz7ndxd"))))
 683     (build-system gnu-build-system)
 684     (native-inputs
 685      (list gobject-introspection pkg-config))
 686     (inputs
 687      (list expat
 688            fftw
 689            giflib
 690            glib
 691            hdf5
 692            imagemagick
 693            lcms
 694            libexif
 695            libgsf
 696            libjpeg-turbo
 697            libpng
 698            librsvg
 699            libtiff
 700            libxml2
 701            libwebp
 702            matio
 703            niftilib
 704            openexr-2
 705            orc
 706            pango
 707            poppler))
 708     (home-page "https://libvips.github.io/libvips/")
 709     (synopsis "Multithreaded image processing system with low memory needs")
 710     (description
 711      "VIPS is a demand-driven, horizontally threaded image processing library.
 712 It's particularly good at processing large images, working with colour,
 713 scientific analysis, and general research & development.
 714
 715 Compared to most image processing libraries VIPS needs little RAM and runs
 716 quickly, especially on machines with more than one CPU core.  This is primarily
 717 due to its architecture which automatically parallelises the image workflows.")
 718     (license license:lgpl2.1+)))
 719
 720 (define-public gmic
 721   (package
 722     (name "gmic")
 723     (version "3.0.0")
 724     (source
 725      (origin
 726        (method url-fetch)
 727        (uri (string-append "https://gmic.eu/files/source/gmic_"
 728                            version ".tar.gz"))
 729        (sha256
 730         (base32 "080inz0wisv3rhvbnzrgcs3j25wq86gybp68yi56gw6vwswnn19z"))))
 731     (build-system cmake-build-system)
 732     (arguments
 733      `(#:tests? #f ;there are no tests
 734        #:configure-flags '("-DBUILD_LIB_STATIC=OFF"
 735                            "-DENABLE_DYNAMIC_LINKING=ON"
 736                            "-DENABLE_LTO=ON")
 737        #:phases
 738        (modify-phases %standard-phases
 739          (add-before 'configure 'set-LDFLAGS
 740            (lambda* (#:key inputs outputs #:allow-other-keys)
 741              (setenv "LDFLAGS"
 742                      (string-append
 743                       "-Wl,-rpath="
 744                       (assoc-ref outputs "out") "/lib")))))))
 745     (native-inputs
 746      (list pkg-config))
 747     (inputs
 748      (list curl
 749            fftw
 750            graphicsmagick
 751            imath
 752            libjpeg-turbo
 753            libpng
 754            libtiff
 755            libx11
 756            ;;opencv ;OpenCV is currently broken in the CI
 757            openexr
 758            zlib))
 759     (home-page "https://gmic.eu/")
 760     (synopsis "Full-featured framework for digital image processing")
 761     (description "G'MIC is a full-featured framework for digital image
 762 processing.  It provides several user interfaces to convert / manipulate
 763 / filter / visualize generic image datasets, ranging from 1D scalar
 764 signals to 3D+t sequences of multi-spectral volumetric images, hence
 765 including 2D color images.")
 766     ;; Dual-licensed, either license applies.
 767     (license (list license:cecill license:cecill-c))))
 768
 769 (define-public gmic-qt
 770   (package
 771     (inherit gmic)
 772     (name "gmic-qt")
 773     (arguments
 774      (substitute-keyword-arguments (package-arguments gmic)
 775        ((#:configure-flags _)
 776         `(list "-DGMIC_QT_HOST=none" "-DENABLE_DYNAMIC_LINKING=ON"
 777                (string-append "-DGMIC_LIB_PATH="
 778                               (assoc-ref %build-inputs "gmic") "/lib")))
 779         ((#:phases phases)
 780          `(modify-phases ,phases
 781             (add-after 'unpack 'qt-chdir
 782               (lambda _ (chdir "gmic-qt") #t))))))
 783     (native-inputs
 784      (list pkg-config qttools-5))
 785     (inputs
 786      (modify-inputs (package-inputs gmic)
 787        (prepend gmic qtbase-5)))
 788     (synopsis "Qt frontend for the G'MIC image processing framework")
 789     (license license:gpl3+)))
 790
 791 (define-public gmic-qt-krita
 792   (package
 793     (inherit gmic-qt)
 794     (name "gmic-qt-krita")
 795     (arguments
 796      (substitute-keyword-arguments (package-arguments gmic-qt)
 797        ((#:configure-flags flags)
 798         '(list "-DGMIC_QT_HOST=krita" "-DENABLE_DYNAMIC_LINKING=ON"
 799                (string-append "-DGMIC_LIB_PATH="
 800                               (assoc-ref %build-inputs "gmic") "/lib")))))
 801     (synopsis "Krita plugin for the G'MIC image processing framework")))
 802
 803 (define-public gmic-qt-gimp
 804   (package
 805     (inherit gmic-qt)
 806     (name "gmic-qt-gimp")
 807     (inputs
 808      ;; GIMP and its dependencies.
 809      (modify-inputs (package-inputs gmic-qt)
 810        (prepend gimp gdk-pixbuf cairo gegl)))
 811     (arguments
 812      (substitute-keyword-arguments (package-arguments gmic-qt)
 813        ((#:configure-flags flags)
 814         '(list "-DGMIC_QT_HOST=gimp" "-DENABLE_DYNAMIC_LINKING=ON"
 815                (string-append "-DGMIC_LIB_PATH="
 816                               (assoc-ref %build-inputs "gmic") "/lib")))))
 817     (synopsis "GIMP plugin for the G'MIC image processing framework")))
 818
 819 (define-public nip2
 820   (package
 821     (name "nip2")
 822     (version "8.7.1")
 823     (source
 824      (origin
 825        (method url-fetch)
 826        (uri (string-append "https://github.com/libvips/nip2/releases/download/v"
 827                            version "/nip2-" version ".tar.gz" ))
 828        (sha256
 829         (base32 "0l7n427njif53npqn02gfjjly8y3khbrkzqxp10j5vp9h97psgiw"))))
 830     (build-system gnu-build-system)
 831     (arguments
 832      `(#:phases
 833        (modify-phases %standard-phases
 834          ;; test_conv.ws keep failing so disabling for now.
 835          (add-after 'unpack 'disable-test-conv
 836            (lambda _
 837              (delete-file "test/workspaces/test_conv.ws")
 838              #t))
 839          (add-before 'check 'set-home
 840            (lambda _
 841              (setenv "HOME" "/tmp") #t)))))
 842     (inputs
 843      `(("vips" ,vips)
 844        ("glib" ,glib)
 845        ("libtiff" ,libtiff)
 846        ("gtk+-2" ,gtk+-2)
 847        ("libxml2" ,libxml2)
 848        ("libexif" ,libexif)
 849        ("libjpeg" ,libjpeg-turbo)        ;required by vips.pc
 850        ("librsvg" ,librsvg)
 851        ("fftw" ,fftw)
 852        ("libgsf" ,libgsf)
 853        ("imagemagick" ,imagemagick)
 854        ("orc" ,orc)
 855        ("matio" ,matio)
 856        ("lcms" ,lcms)
 857        ("libwebp" ,libwebp)
 858        ("openexr" ,openexr-2)
 859        ("poppler" ,poppler)
 860        ("gsl" ,gsl)))
 861     (native-inputs
 862      (list flex bison pkg-config))
 863     (home-page "https://github.com/libvips/nip2")
 864     (synopsis "Spreadsheet-like GUI for libvips")
 865     (description "This package provide a graphical user interface (GUI) for
 866 the VIPS image processing library.  It's a little like a spreadsheet: you
 867 create a set of formula connecting your objects together, and on a change nip2
 868 recalculates.")
 869     (license license:gpl2+)))
 870
 871 (define-public vxl
 872   (package
 873     (name "vxl")
 874     (version "2.0.2")
 875     (source
 876      (origin
 877        (method git-fetch)
 878        (uri (git-reference
 879              (url "https://github.com/vxl/vxl")
 880              (commit (string-append "v" version))))
 881        (file-name (git-file-name name version))
 882        (sha256
 883         (base32 "0949hw57szq8943f1whwqaz591xjmb19kj803hcv74hdai2b0ycg"))
 884        (modules '((guix build utils)))
 885        ;; TODO: vxl includes an old version of dcmtk.  It won't build with
 886        ;; version 3.6.x.
 887        (snippet
 888         '(begin
 889            (for-each delete-file-recursively
 890                      '("v3p/bzlib/"
 891                        "v3p/geotiff/"
 892                        "v3p/jpeg/"
 893                        "v3p/png/"
 894                        "v3p/tiff/"
 895                        "v3p/zlib/"))
 896            (substitute* "v3p/CMakeLists.txt"
 897              (("add_subdirectory\\((tiff|png|jpeg|zlib|bzlib|geotiff)\\)")
 898               ""))
 899            #t))))
 900     (build-system cmake-build-system)
 901     (inputs
 902      (list libgeotiff libtiff libjpeg-turbo libpng zlib))
 903     (home-page "https://github.com/vxl/vxl/")
 904     (synopsis "Collection of C++ libraries for computer vision")
 905     (description "VXL (the Vision-something-Libraries) is a collection of C++
 906 libraries designed for computer vision research and implementation.")
 907     (license license:bsd-3)))
 908
 909 (define-public vxl-1
 910   (package (inherit vxl)
 911     (name "vxl")
 912     (version "1.18.0")
 913     (source
 914      (origin
 915        (method git-fetch)
 916        (uri (git-reference
 917              (url "https://github.com/vxl/vxl")
 918              (commit (string-append "v" version))))
 919        (file-name (git-file-name name version))
 920        (sha256
 921         (base32 "1g4mr2cc58jwm0vasscbd4y5380wj3ahkvq121z4gs83fhavvxgz"))
 922        (modules '((guix build utils)))
 923        (snippet
 924         '(begin
 925            (for-each delete-file-recursively
 926                      '("v3p/bzlib/"
 927                        "v3p/geotiff/"
 928                        "v3p/png/"
 929                        "v3p/tiff/"
 930                        "v3p/zlib/"))
 931            (substitute* "v3p/CMakeLists.txt"
 932              (("add_subdirectory\\((tiff|png|jpeg|zlib|bzlib|geotiff)\\)")
 933               ""))
 934            #t))))
 935     (arguments
 936      `(#:configure-flags
 937        ;; Needed for itk-snap
 938        (list "-DVNL_CONFIG_LEGACY_METHODS=ON")))))
 939
 940 (define-public insight-toolkit
 941   (package
 942     (name "insight-toolkit")
 943     (version "5.0.0")
 944     (source
 945      (origin
 946        (method url-fetch)
 947        (uri (string-append "https://github.com/InsightSoftwareConsortium/ITK/"
 948                            "releases/download/v" version "/InsightToolkit-"
 949                            version ".tar.xz"))
 950        (sha256
 951         (base32 "0bs63mk4q8jmx38f031jy5w5n9yy5ng9x8ijwinvjyvas8cichqi"))))
 952     (build-system cmake-build-system)
 953     (arguments
 954      `(#:tests? #f            ; tests require network access and external data
 955        #:configure-flags
 956        '("-DITK_USE_GPU=ON"
 957          "-DITK_USE_SYSTEM_LIBRARIES=ON"
 958          "-DITK_USE_SYSTEM_GOOGLETEST=ON"
 959          "-DITK_BUILD_SHARED=ON"
 960          ;; This prevents "GTest::GTest" from being added to the ITK_LIBRARIES
 961          ;; variable in the installed CMake files.  This is necessary as other
 962          ;; packages using insight-toolkit could not be configured otherwise.
 963          "-DGTEST_ROOT=gtest")
 964
 965        #:phases
 966        (modify-phases %standard-phases
 967          (add-after 'unpack 'do-not-tune
 968            (lambda _
 969              (substitute* "CMake/ITKSetStandardCompilerFlags.cmake"
 970                (("-mute=native") ""))
 971              #t)))))
 972     (inputs
 973      `(("eigen" ,eigen)
 974        ("expat" ,expat)
 975        ("fftw" ,fftw)
 976        ("fftwf" ,fftwf)
 977        ("hdf5" ,hdf5)
 978        ("libjpeg" ,libjpeg-turbo)
 979        ("libpng" ,libpng)
 980        ("libtiff" ,libtiff)
 981        ("mesa" ,mesa-opencl)
 982        ("perl" ,perl)
 983        ("python" ,python)
 984        ("tbb" ,tbb)
 985        ("vxl" ,vxl-1)
 986        ("zlib" ,zlib)))
 987     (native-inputs
 988      (list googletest pkg-config))
 989     (home-page "https://github.com/InsightSoftwareConsortium/ITK/")
 990     (synopsis "Scientific image processing, segmentation and registration")
 991     (description "The Insight Toolkit (ITK) is a toolkit for N-dimensional
 992 scientific image processing, segmentation, and registration.  Segmentation is
 993 the process of identifying and classifying data found in a digitally sampled
 994 representation.  Typically the sampled representation is an image acquired
 995 from such medical instrumentation as CT or MRI scanners.  Registration is the
 996 task of aligning or developing correspondences between data.  For example, in
 997 the medical environment, a CT scan may be aligned with a MRI scan in order to
 998 combine the information contained in both.")
 999     (license license:asl2.0)))
1000
1001 (define-public insight-toolkit-4
1002   (package (inherit insight-toolkit)
1003     (version "4.13.2")
1004     (source
1005      (origin
1006        (method url-fetch)
1007        (uri (string-append "https://github.com/InsightSoftwareConsortium/ITK/"
1008                            "releases/download/v" version "/InsightToolkit-"
1009                            version ".tar.xz"))
1010        (sha256
1011         (base32 "19cgfpd63gqrvc3m27m394gy2d7w79g5y6lvznb5qqr49lihbgns"))))
1012     (arguments
1013      `(#:tests? #f            ; tests require network access and external data
1014        #:configure-flags
1015        '("-DITKV3_COMPATIBILITY=ON"     ; needed for itk-snap
1016          "-DITK_USE_GPU=ON"
1017          "-DITK_USE_SYSTEM_LIBRARIES=ON"
1018          "-DITK_USE_SYSTEM_GOOGLETEST=ON"
1019          "-DITK_USE_SYSTEM_VXL=ON")))))
1020
1021 (define-public insight-toolkit-4.12
1022   (package (inherit insight-toolkit-4)
1023     (version "4.12.2")
1024     (source
1025      (origin
1026        (method url-fetch)
1027        (uri (string-append "mirror://sourceforge/itk/itk/4.12/"
1028                            "InsightToolkit-" version ".tar.xz"))
1029        (sha256
1030         (base32 "1qw9mxbh083siljygahl4gdfv91xvfd8hfl7ghwii19f60xrvn2w"))))))
1031
1032 (define-public itk-snap
1033   (package
1034     (name "itk-snap")
1035     (version "3.8.0")
1036     (source
1037      (origin
1038        (method git-fetch)
1039        (uri (git-reference
1040              (url "https://git.code.sf.net/p/itk-snap/src")
1041              (commit (string-append "v" version))))
1042        (file-name (git-file-name name version))
1043        (sha256
1044         (base32 "15i5ixpryfrbf3vrrb5rici8fb585f25k0v1ljds16bp1f1msr4q"))
1045        (patches (search-patches "itk-snap-alt-glibc-compat.patch"))))
1046     (build-system cmake-build-system)
1047     (arguments
1048      `(#:configure-flags
1049        (list "-DSNAP_VERSION_GIT_SHA1=release"
1050              "-DSNAP_VERSION_GIT_BRANCH=release"
1051              "-DSNAP_VERSION_GIT_TIMESTAMP=0"
1052              "-DSNAP_PACKAGE_QT_PLUGINS=OFF"
1053              "-DCMAKE_POSITION_INDEPENDENT_CODE=ON")
1054        #:phases
1055        (modify-phases %standard-phases
1056          ;; During the installation phase all libraries provided by all
1057          ;; dependencies will be copied to the lib directory.  That's insane,
1058          ;; so we disable this.
1059          (add-after 'unpack 'do-not-copy-dependencies
1060            (lambda _
1061              (substitute* "CMakeLists.txt"
1062                (("install_qt5_executable\
1063 \\(\\$\\{SNAP_MAIN_INSTALL_DIR\\}/\\$\\{SNAP_EXE\\}\\)")
1064                 ""))))
1065          (add-after 'unpack 'disable-gui-tests
1066            (lambda _
1067              ;; The GUI tests just time out.
1068              (substitute* "CMakeLists.txt"
1069                (("  (Workspace|DiffSpace|ProbeIntensity|RegionCompetition\
1070 |RandomForest|RandomForestBailOut)")
1071                 ""))))
1072          (add-after 'unpack 'make-reproducible
1073            (lambda _
1074              (substitute* "CMakeLists.txt"
1075                (("TODAY\\(SNAP_VERSION_COMPILE_DATE\\)")
1076                 "SET(SNAP_VERSION_COMPILE_DATE \"(removed for reproducibility)\")"))))
1077          (add-after 'unpack 'prepare-submodules
1078            (lambda* (#:key inputs #:allow-other-keys)
1079              (rmdir "Submodules/c3d")
1080              (copy-recursively (assoc-ref inputs "c3d-src")
1081                                "Submodules/c3d")
1082              (substitute* '("Submodules/c3d/adapters/BiasFieldCorrectionN4.cxx"
1083                             "Submodules/c3d/adapters/ApplyMetric.cxx")
1084                (("vcl_") "std::"))
1085              (rmdir "Submodules/greedy")
1086              (symlink (assoc-ref inputs "greedy-src")
1087                       "Submodules/greedy")))
1088          (add-after 'unpack 'fix-includes
1089            (lambda _
1090              (substitute* "GUI/Model/RegistrationModel.cxx"
1091                (("<vnl_symmetric_eigensystem.h>")
1092                 "<vnl/algo/vnl_symmetric_eigensystem.h>"))))
1093          (add-before 'check 'prepare-tests
1094            (lambda _
1095              ;; Needed by at least one test.
1096              (setenv "HOME" "/tmp")))
1097          (add-after 'install 'wrap-executable
1098            (lambda* (#:key inputs outputs #:allow-other-keys)
1099              (let ((out (assoc-ref outputs "out")))
1100                (wrap-program (string-append out "/bin/itksnap")
1101                  `("QT_PLUGIN_PATH" ":" prefix
1102                    ,(map (lambda (label)
1103                            (string-append (assoc-ref inputs label)
1104                                           "/lib/qt5/plugins"))
1105                          '("qtbase" "qtdeclarative-5"))))))))))
1106     (inputs
1107      (list curl
1108            fftw
1109            fftwf
1110            glu
1111            hdf5
1112            mesa-opencl
1113            ;; This package does not build with either insight-toolkit 5.0.0
1114            ;; and not with 4.13.  It really needs to be 4.12.
1115            insight-toolkit-4.12
1116            vtk-7
1117            qtbase-5
1118            qtdeclarative-5
1119            vxl-1
1120            zlib))
1121     (native-inputs
1122      `(("googletest" ,googletest)
1123        ("qttools-5" ,qttools-5)
1124        ("pkg-config" ,pkg-config)
1125        ("c3d-src"
1126         ,(let* ((commit "f521358db26e00002c911cc47bf463b043942ad3")
1127                 (revision "1")
1128                 (version (git-version "0" revision commit)))
1129            (origin
1130              (method git-fetch)
1131              (uri (git-reference
1132                    (url "https://github.com/pyushkevich/c3d")
1133                    (commit commit)))
1134              (file-name (git-file-name "c3d" version))
1135              (sha256
1136               (base32
1137                "0kyv3rxrxwr8c3sa9zv01lsnhk95b27gx1s870k3yi8qp52h7bx3")))))
1138        ;; We are using an arbitrary commit from 2017 because the latest
1139        ;; version breaks the build...
1140        ("greedy-src"
1141         ,(let* ((commit "97e340f7e8e66597599144947775e6039e79a0d3")
1142                 (revision "1")
1143                 (version (git-version "0" revision commit)))
1144            (origin
1145              (method git-fetch)
1146              (uri (git-reference
1147                    (url "https://github.com/pyushkevich/greedy")
1148                    (commit commit)))
1149              (file-name (git-file-name "greedy" version))
1150              (sha256
1151               (base32
1152                "0k5bc9za4jrc8z9dj08z1rkcp5xf0gnd1d2jmi1w9ny4vxh2q2ab")))))))
1153     (home-page "https://sourceforge.net/p/itk-snap/")
1154     (synopsis "Medical image segmentation")
1155     (description "ITK-SNAP is a tool for segmenting anatomical structures in
1156 medical images.  It provides an automatic active contour segmentation
1157 pipeline, along with supporting a manual segmentation toolbox.  ITK-SNAP has a
1158 full-featured UI aimed at clinical researchers.")
1159     ;; This includes the submodules greedy and c3d.
1160     (license license:gpl3+)))
1161
1162 (define-public metapixel
1163   ;; Follow stable branch.
1164   (let ((commit "98ee9daa093b6c334941242e63f90b1c2876eb4f"))
1165     (package
1166       (name "metapixel")
1167       (version (git-version "1.0.2" "1" commit))
1168       (source
1169        (origin
1170          (method git-fetch)
1171          (uri (git-reference
1172                (url "https://github.com/schani/metapixel")
1173                (commit commit)
1174                ;; TODO: Package rwimg and lispreader?
1175                (recursive? #t)))
1176          (file-name (git-file-name name version))
1177          (sha256
1178           (base32 "0r7n3a6bvcxkbpda4mwmrpicii09iql5z69nkjqygkwxw7ny3309"))))
1179       (build-system gnu-build-system)
1180       (inputs
1181        `(("giflib" ,giflib)
1182          ("libjpeg" ,libjpeg-turbo)
1183          ("libpng" ,libpng)
1184          ("perl" ,perl)))
1185       (native-inputs
1186        `(("pkg-config" ,pkg-config)
1187          ("docbook-xml" ,docbook-xml)
1188          ("docbook-xsl" ,docbook-xsl)
1189          ("xsltproc" ,libxslt)))
1190       (arguments
1191        `(#:tests? #f                    ; No tests.
1192          #:make-flags (list
1193                        (string-append "PREFIX=" (assoc-ref %outputs "out"))
1194                        (string-append "MANPAGE_XSL="
1195                                       (assoc-ref %build-inputs "docbook-xsl")
1196                                       "/xml/xsl/docbook-xsl-*/manpages/docbook.xsl"))
1197          #:phases
1198          (modify-phases %standard-phases
1199            (delete 'configure)
1200            (add-before 'install 'make-local-docbook-xml
1201              (lambda* (#:key inputs #:allow-other-keys)
1202                (substitute* "metapixel.xml"
1203                  (("http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd")
1204                   (string-append (assoc-ref inputs "docbook-xml")
1205                                  "/xml/dtd/docbook/docbookx.dtd")))
1206                #t))
1207            (add-before 'install 'fix-directory-creation
1208              (lambda* (#:key outputs #:allow-other-keys)
1209                (mkdir-p (string-append (assoc-ref outputs "out") "/share/man/man1"))
1210                #t)))))
1211       (home-page "https://www.complang.tuwien.ac.at/schani/metapixel/")
1212       (synopsis "Photomosaics generator")
1213       (description "Metapixel is a program for generating photomosaics.  It can
1214 generate classical photomosaics, in which the source image is viewed as a
1215 matrix of equally sized rectangles for each of which a matching image is
1216 substituted, as well as collage-style photomosaics, in which rectangular parts
1217 of the source image at arbitrary positions (i.e. not aligned to a matrix) are
1218 substituted by matching images.")
1219       (license license:gpl2))))
1220
1221 (define-public scantailor-advanced
1222   (let ((commit "3d1e74e6ace413733511086934a66f4e3f7a6027"))
1223     (package
1224       (name "scantailor-advanced")
1225       (version (string-append "1.0.16-" (string-take commit 7)))
1226       (source
1227        (origin
1228          (method git-fetch)
1229          (uri (git-reference
1230                (url "https://github.com/4lex4/scantailor-advanced")
1231                (commit commit)))
1232          (file-name (git-file-name name version))
1233          (sha256
1234           (base32
1235            "0kixwjb2x457dq7927hkh34c803p7yh1pmn6n61rk9shqrcg492h"))))
1236       (build-system qt-build-system)
1237       (native-inputs
1238        (list qttools-5))
1239       (inputs
1240        `(("boost" ,boost)
1241          ("libjpeg" ,libjpeg-turbo)
1242          ("libpng" ,libpng)
1243          ("libtiff" ,libtiff)
1244          ("qtbase" ,qtbase-5)
1245          ("qtsvg-5" ,qtsvg-5)
1246          ("zlib" ,zlib)))
1247       (arguments
1248        `(#:phases
1249          (modify-phases %standard-phases
1250            ;; Some tests require a display and fail with offscreen mode.
1251            (add-after 'unpack 'disable-failing-tests
1252              (lambda _
1253                (setenv "ARGS" "--exclude-regex \"imageproc_.*\"")
1254                #t)))))
1255       (home-page "https://github.com/4lex4/scantailor-advanced")
1256       (synopsis "Clean up scanned pages")
1257       (description "Scan Tailor is an interactive post-processing tool for
1258 scanned pages.  It performs operations such as page splitting, deskewing,
1259 adding/removing borders, and others.  You give it raw scans, and you get pages
1260 ready to be printed or assembled into a PDF or DJVU file.  Scanning, optical
1261 character recognition, and assembling multi-page documents are out of scope of
1262 this project.
1263
1264 Scan Tailer Advanced is a fork of Scan Tailer that merges Scan Tailor Featured
1265 and Scan Tailor Enhanced versions as well as including many more bug fixes.")
1266       (license license:gpl3+))))
1267
1268 (define-public stiff
1269   (package
1270     (name "stiff")
1271     (version "2.4.0")
1272     (source
1273      (origin
1274        (method url-fetch)
1275        (uri (string-append "https://www.astromatic.net/download/stiff/stiff-"
1276                            version ".tar.gz"))
1277        (sha256
1278         (base32 "14m92dskzw7bwsr64ha4p0mj3ndv13gwcbfic3qxrs3zq5353s7l"))))
1279     (build-system gnu-build-system)
1280     (inputs
1281      (list libtiff zlib libjpeg-turbo))
1282     (home-page "https://www.astromatic.net/software/stiff")
1283     (synopsis "Convert scientific FITS images to TIFF format")
1284     (description
1285      "STIFF is a program that converts scientific @acronym{FITS, Flexible Image
1286 Transport System} images to the more popular TIFF format for illustration
1287 purposes.")
1288     (license license:gpl3+)))
1289
1290 (define-public python-imgviz
1291   (package
1292     (name "python-imgviz")
1293     (version "1.2.6")
1294     (source
1295      (origin
1296        ;; PyPi tarball lacks tests.
1297        (method git-fetch)
1298        (uri (git-reference
1299              (url "https://github.com/wkentaro/imgviz.git")
1300              (commit (string-append "v" version))))
1301        (file-name (git-file-name name version))
1302        (sha256
1303         (base32 "1bm0wdv5p26i8nl4kx3145cz553v401sgbpgc96sddzjfmfiydcw"))))
1304     (build-system python-build-system)
1305     (arguments
1306      `(#:phases
1307        (modify-phases %standard-phases
1308          (replace 'check
1309            (lambda* (#:key inputs outputs tests? #:allow-other-keys)
1310              (when tests?
1311                (add-installed-pythonpath inputs outputs)
1312                (invoke "pytest" "-v" "tests"))
1313              #t)))))
1314     (propagated-inputs
1315       (list python-matplotlib python-numpy python-pillow python-pyyaml))
1316     (native-inputs (list python-pytest))
1317     (home-page "http://github.com/wkentaro/imgviz")
1318     (synopsis "Image Visualization Tools")
1319     (description "Python library for object detection, semantic and instance
1320 segmentation.")
1321     (license license:expat)))
1322
1323 (define-public labelme
1324   (package
1325     (name "labelme")
1326     (version "4.5.13")
1327     (source
1328      (origin
1329        ;; PyPi tarball lacks tests.
1330        (method git-fetch)
1331        (uri (git-reference
1332              (url "https://github.com/wkentaro/labelme.git")
1333              (commit (string-append "v" version))))
1334        (file-name (git-file-name name version))
1335        (sha256
1336         (base32 "0cmi2xb4dgh7738l259rgwhn9l134f0vnaaqc2gflc5yr3lqhrv2"))))
1337     (build-system python-build-system)
1338     (arguments
1339      `(#:phases
1340        (modify-phases %standard-phases
1341          (add-after 'unpack 'loosen-requirements
1342            (lambda _
1343              ;; Don't require an outdated version of matplotlib.
1344              (substitute* "setup.py"
1345                (("matplotlib<3\\.3")
1346                 "matplotlib"))))
1347          (add-before 'check 'start-xserver
1348            (lambda* (#:key inputs #:allow-other-keys)
1349              (let ((xorg-server (assoc-ref inputs "xorg-server")))
1350                ;; Options taken from CI workflow.
1351                (system (string-append xorg-server "/bin/Xvfb :99 -screen 0 "
1352                                       "1920x1200x24 -ac +extension GLX +render "
1353                                       "-noreset &"))
1354                (setenv "DISPLAY" ":99.0"))))
1355          (replace 'check
1356            (lambda* (#:key inputs outputs tests? #:allow-other-keys)
1357              (when tests?
1358                (add-installed-pythonpath inputs outputs)
1359                ;; Fails when invoking help2man for unknown reason.
1360                (delete-file "tests/docs_tests/man_tests/test_labelme_1.py")
1361                ;; One test hangs.
1362                (delete-file "tests/labelme_tests/widgets_tests/test_label_dialog.py")
1363                ;; Calls incompatible function signatures.
1364                (delete-file "tests/labelme_tests/widgets_tests/test_label_list_widget.py")
1365                (setenv "MPLBACKEND" "agg")
1366                (invoke "pytest" "-v" "tests" "-m" "not gpu")))))))
1367     (propagated-inputs
1368       (list python-imgviz
1369             python-matplotlib
1370             python-numpy
1371             python-pillow
1372             python-pyyaml
1373             python-qtpy
1374             python-termcolor))
1375     (native-inputs
1376       (list python-pytest python-pytest-qt xorg-server-for-tests))
1377     (home-page "https://github.com/wkentaro/labelme")
1378     (synopsis
1379       "Image Polygonal Annotation")
1380     (description
1381       "Image and video labeling tool supporting different shapes like
1382 polygons, rectangles, circles, lines, points and VOC/COCO export.")
1383     (license license:gpl3+)))