guix/gnu/packages/image-processing.scm

;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2017 John Darrington <jmd@gnu.org>
;;; Copyright © 2017, 2019, 2022 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2014, 2021-2022 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2014 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2018–2021 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
;;; Copyright © 2018 Lprndn <guix@lprndn.info>
;;; Copyright © 2019, 2021 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
;;; Copyright © 2020, 2021 Vinicius Monego <monego@posteo.net>
;;; Copyright © 2020 Pierre Neidhardt <mail@ambrevar.xyz>
;;; Copyright © 2020 Brendan Tildesley <mail@brendan.scot>
;;; Copyright © 2021 Oleh Malyi <astroclubzp@gmail.com>
;;; Copyright © 2021, 2022 Felix Gruber <felgru@posteo.net>
;;; Copyright © 2021 Andy Tai <atai@atai.org>
;;; Copyright © 2021 Ekaitz Zarraga <ekaitz@elenq.tech>
;;; Copyright © 2021 Paul Garlick <pgarlick@tourbillion-technology.com>
;;; Copyright © 2021 Guillaume Le Vaillant <glv@posteo.net>
;;; Copyright © 2021 Ivan Gankevich <i.gankevich@spbu.ru>
;;; Copyright © 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2022 Tomasz Jeneralczyk <tj@schwi.pl>
;;; Copyright © 2022 Paul A. Patience <paul@apatience.com>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

(define-module (gnu packages image-processing)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix packages)
  #:use-module (guix gexp)
  #:use-module (guix utils)
  #:use-module (guix download)
  #:use-module (guix git-download)
  #:use-module (guix build-system qt)
  #:use-module (guix build-system cmake)
  #:use-module (guix build-system gnu)
  #:use-module (guix build-system python)
  #:use-module (gnu packages)
  #:use-module (gnu packages algebra)
  #:use-module (gnu packages bison)
  #:use-module (gnu packages boost)
  #:use-module (gnu packages check)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages cpp)
  #:use-module (gnu packages curl)
  #:use-module (gnu packages docbook)
  #:use-module (gnu packages documentation)
  #:use-module (gnu packages flex)
  #:use-module (gnu packages fontutils)
  #:use-module (gnu packages game-development)
  #:use-module (gnu packages gcc)
  #:use-module (gnu packages geo)
  #:use-module (gnu packages ghostscript)
  #:use-module (gnu packages gimp)
  #:use-module (gnu packages gl)
  #:use-module (gnu packages glib)
  #:use-module (gnu packages gnome)
  #:use-module (gnu packages graphics)
  #:use-module (gnu packages graphviz)
  #:use-module (gnu packages gstreamer)
  #:use-module (gnu packages gtk)
  #:use-module (gnu packages icu4c)
  #:use-module (gnu packages image)
  #:use-module (gnu packages imagemagick)
  #:use-module (gnu packages linux)
  #:use-module (gnu packages maths)
  #:use-module (gnu packages mpi)
  #:use-module (gnu packages pdf)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages photo)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages pretty-print)
  #:use-module (gnu packages protobuf)
  #:use-module (gnu packages python)
  #:use-module (gnu packages python-check)
  #:use-module (gnu packages python-science)
  #:use-module (gnu packages python-xyz)
  #:use-module (gnu packages qt)
  #:use-module (gnu packages sdl)
  #:use-module (gnu packages serialization)
  #:use-module (gnu packages sphinx)
  #:use-module (gnu packages sqlite)
  #:use-module (gnu packages tbb)
  #:use-module (gnu packages textutils)
  #:use-module (gnu packages tls)
  #:use-module (gnu packages version-control)
  #:use-module (gnu packages video)
  #:use-module (gnu packages xiph)
  #:use-module (gnu packages xml)
  #:use-module (gnu packages xorg)
  #:use-module (ice-9 match)
  #:use-module (srfi srfi-1))

;; TODO: this is not reproducible.
(define-public bart
  (package
    (name "bart")
    (version "0.8.00")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/mrirecon/bart")
             (commit "eacc67b95cf128487ecc48f0e6541ea4dca08818")))
       (file-name (git-file-name name version))
       (sha256
        (base32 "05lcf7c3g7ms5h82bw1mi4kzkdv5wpqi1zrfhqfkgbcpd3irj6aq"))))
    (build-system gnu-build-system)
    (arguments
     (list
      #:test-target "utest"
      #:make-flags #~(list
                      (string-append "PREFIX=" #$output)
                      "PARALLEL=1"
                      "PARALLEL_NJOBS=1"
                      "OPENBLAS=1"
                      "SCALAPACK=1"
                      (string-append "BLAS_BASE=" #$(this-package-input "openblas"))
                      (string-append "FFTW_BASE=" #$(this-package-input "fftw")))
      #:parallel-build? #false ;leads to non-deterministic output
      #:phases
      #~(modify-phases %standard-phases
          (delete 'configure)
          (add-after 'unpack 'patch-/bin/bash
            (lambda _
              (substitute* "tests/pics.mk"
                (("/bin/bash") (which "bash"))))))))
    (inputs
     (list fftw
           fftwf
           libpng
           openblas
           python
           scalapack))
    (native-inputs
     (list doxygen
           util-linux)) ;for flock
    (home-page "https://mrirecon.github.io/bart/")
    (synopsis "Toolbox for computational magnetic resonance imaging")
    (description "The Berkeley Advanced Reconstruction Toolbox (BART) is an
image-reconstruction framework for Computational Magnetic Resonance Imaging.
The tools in this software implement various reconstruction algorithms for
Magnetic Resonance Imaging.")
    (license license:bsd-3)))

(define-public dcmtk
  (package
    (name "dcmtk")
    (version "3.6.7")
    (source
     (origin
       (method url-fetch)
       (uri
        (string-append "ftp://dicom.offis.de/pub/dicom/offis/software/dcmtk/"
                       "dcmtk" (string-join (string-split version #\.) "")
                       "/dcmtk-" version ".tar.gz"))
       (sha256
        (base32 "02kix73qhndgb56cmi5327666i6imp7hi17wwqp26q4d7s72jn3w"))))
    (build-system cmake-build-system)
    (arguments
     ;; By default, only static archives are built.
     (list #:configure-flags #~(list "-DBUILD_SHARED_LIBS=ON")))
    (inputs
     (list icu4c
           libjpeg-turbo
           libpng
           libtiff
           libxml2
           openssl
           zlib))
    (native-inputs
     (list doxygen))           ; for HTML documentation
    (home-page "https://dcmtk.org")
    (synopsis "Libraries and programs implementing parts of the DICOM standard")
    (description "DCMTK is a collection of libraries and applications
implementing large parts the DICOM standard.  It includes software for
examining, constructing and converting DICOM image files, handling offline
media, sending and receiving images over a network connection, as well as
demonstrative image storage and worklist servers.")
    (license (license:fsf-free
              "file://COPYRIGHT"
              "A union of the Apache 2.0 licence and various non-copyleft
licences similar to the Modified BSD licence."))))

(define-public mia
  (package
    (name "mia")
    (version "2.4.7")
    (source (origin
              (method url-fetch)
              (uri (string-append "mirror://sourceforge/mia/mia/"
                                  (version-major+minor version)
                                  "/mia-" version ".tar.xz"))
              (sha256
               (base32
                "0qpcd3n26q52dpyibm11f5l6cgscdr54p2jish39gc3p1f5h3ws1"))
              (patches (search-patches "mia-fix-boost-headers.patch"
                                       "mia-vtk9.patch"
                                       "mia-vtk92.patch"
                                       "mia-vtk-version.patch"))))
    (build-system cmake-build-system)
    (arguments
     `(#:configure-flags
       (list "-DMIA_CREATE_NIPYPE_INTERFACES=OFF"
             "-DCMAKE_CXX_FLAGS=-fpermissive")))
    (inputs
     (list boost
           dcmtk
           doxygen
           eigen
           fftw
           fftwf
           gsl
           gts
           hdf5
           itpp
           libjpeg-turbo
           libpng
           libtiff
           libxml2
           libxml++
           maxflow
           niftilib
           nlopt
           openexr-2
           python-lxml
           vtk))
    (native-inputs
     (list pkg-config
           python-wrapper))
    (home-page "http://mia.sourceforge.net")
    (synopsis "Toolkit for gray scale medical image analysis")
    (description "MIA provides a combination of command line tools, plug-ins,
and libraries that make it possible run image processing tasks interactively
in a command shell and to prototype using the shell's scripting language.  It
is built around a plug-in structure that makes it easy to add functionality
without compromising the original code base and it makes use of a wide variety
of external libraries that provide additional functionality.")
    (license license:gpl3+)))

(define-public opencolorio
  (package
    (name "opencolorio")
    (version "1.1.1")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/AcademySoftwareFoundation/OpenColorIO")
             (commit (string-append "v" version))))
       (sha256
        (base32 "12srvxca51czpfjl0gabpidj9n84mw78ivxy5w75qhq2mmc798sb"))
       (file-name (git-file-name name version))
       (modules '((guix build utils)))
       (snippet
        `(begin
           ;; Remove bundled tarballs, patches, and .jars(!).  XXX: Upstream
           ;; claims to have fixed USE_EXTERNAL_YAML, but it still fails with:
           ;; https://github.com/AcademySoftwareFoundation/OpenColorIO/issues/517
           ;; When removing it, also remove it from the licence field comment.
           (for-each delete-file-recursively
                     (filter
                      (lambda (full-name)
                        (let ((file (basename full-name)))
                          (not (or (string-prefix? "yaml-cpp-0.3" file)
                                   (string=? "unittest.h" file)))))
                      (find-files "ext" ".*")))

           #t))))
    (build-system cmake-build-system)
    (arguments
     `(#:configure-flags
       (list (string-append "-DCMAKE_CXX_FLAGS="
                            "-Wno-error=deprecated-declarations "
                            "-Wno-error=unused-function")
             "-DOCIO_BUILD_STATIC=OFF"
             ;; "-DUSE_EXTERNAL_YAML=ON"
             "-DUSE_EXTERNAL_TINYXML=ON"
             "-DUSE_EXTERNAL_LCMS=ON")
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'patch-test-suite
           (lambda _
             (substitute* "src/core_tests/CMakeLists.txt"
               (("/bin/sh") (which "bash")))
             #t)))))
    (native-inputs
     (list git pkg-config))
    (inputs
     ;; XXX Adding freeglut, glew, ilmbase, mesa, and openimageio for
     ;; ocioconvert fails: error: conflicting declaration ?typedef void
     ;; (* PFNGLGETFRAGMENTMATERIALFVSGIXPROC)(GLenum, GLenum, GLfloat*)
     (list lcms openexr-2 tinyxml))
    (home-page "https://opencolorio.org")
    (synopsis "Color management for visual effects and animation")
    (description
     "OpenColorIO, or OCIO, is a complete color management solution geared
towards motion picture production, with an emphasis on visual effects and
computer animation.  It provides a straightforward and consistent user
experience across all supporting applications while allowing for sophisticated
back-end configuration options suitable for high-end production usage.

OCIO is compatible with the @acronym{ACES, Academy Color Encoding
Specification} and is @acronym{LUT, look-up table}-format agnostic, supporting
many popular formats.")
    (license (list license:expat        ; docs/ociotheme/static, ext/yaml-cpp-*
                   license:zlib         ; src/core/md5
                   license:bsd-3))))    ; the rest

(define-public vtk
  (package
    (name "vtk")
    (version "9.2.2")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://vtk.org/files/release/"
                                  (version-major+minor version)
                                  "/VTK-" version ".tar.gz"))
              (sha256
               (base32
                "0x8h2bwxq2870067j7wqd0qym87pa3inkbri93zrdb0zwwmhlnqw"))
              (modules '((guix build utils)))
              (snippet
               '(begin
                  (for-each
                   (lambda (dir)
                     (delete-file-recursively
                      (string-append "ThirdParty/" dir "/vtk" dir)))
                   ;; pugixml depended upon unconditionally
                   '("doubleconversion" "eigen" "expat" "freetype" "gl2ps"
                     "glew" "hdf5" "jpeg" "jsoncpp" "libharu" "libproj"
                     "libxml2" "lz4" "netcdf" "ogg" "png" "sqlite" "theora"
                     "tiff" "zlib"))
                  (substitute* "IO/ExportPDF/vtkPDFContextDevice2D.cxx"
                    (("\\bHPDF_UINT16 (noPen|dash|dot|denseDot|dashDot|dashDotDot)\\b"
                      _ var)
                     (string-append "HPDF_REAL " var)))))))
    (properties `((release-monitoring-url . "https://vtk.org/download/")))
    (build-system cmake-build-system)
    (arguments
     '(#:build-type "Release"           ;Build without '-g' to save space.
       #:configure-flags '(;"-DBUILD_TESTING:BOOL=TRUE"
                           ;    ; not honored
                           "-DVTK_USE_EXTERNAL=OFF" ;; default
                           "-DVTK_MODULE_USE_EXTERNAL_VTK_doubleconversion=ON"
                           "-DVTK_MODULE_USE_EXTERNAL_VTK_eigen=ON"
                           "-DVTK_MODULE_USE_EXTERNAL_VTK_expat=ON"
                           "-DVTK_MODULE_USE_EXTERNAL_VTK_freetype=ON"
                           "-DVTK_MODULE_USE_EXTERNAL_VTK_gl2ps=ON"
                           "-DVTK_MODULE_USE_EXTERNAL_VTK_glew=ON"
                           "-DVTK_MODULE_USE_EXTERNAL_VTK_hdf5=ON"
                           "-DVTK_MODULE_USE_EXTERNAL_VTK_jpeg=ON"
                           "-DVTK_MODULE_USE_EXTERNAL_VTK_jsoncpp=ON"
                           "-DVTK_MODULE_USE_EXTERNAL_VTK_libharu=ON"
                           "-DVTK_MODULE_USE_EXTERNAL_VTK_libproj=ON"
                           "-DVTK_MODULE_USE_EXTERNAL_VTK_libxml2=ON"
                           "-DVTK_MODULE_USE_EXTERNAL_VTK_lz4=ON"
                           "-DVTK_MODULE_USE_EXTERNAL_VTK_netcdf=ON"
                           "-DVTK_MODULE_USE_EXTERNAL_VTK_ogg=ON"
                           "-DVTK_MODULE_USE_EXTERNAL_VTK_png=ON"
                           ;"-DVTK_MODULE_USE_EXTERNAL_VTK_pugixml=ON"    ; breaks IO/CityGML
                           "-DVTK_MODULE_USE_EXTERNAL_VTK_sqlite=ON"
                           "-DVTK_MODULE_USE_EXTERNAL_VTK_theora=ON"
                           "-DVTK_MODULE_USE_EXTERNAL_VTK_tiff=ON"
                           "-DVTK_MODULE_USE_EXTERNAL_VTK_zlib=ON"
                           "-DVTK_MODULE_ENABLE_VTK_RenderingExternal=YES" ; For F3D
                           "-DVTK_WRAP_PYTHON=ON"
                           "-DVTK_PYTHON_VERSION:STRING=3"
                           )
       #:tests? #f))        ;XXX: test data not included
    (inputs
     (list double-conversion
           eigen
           expat
           freetype
           gl2ps
           glew
           glu
           hdf5
           libharu
           libjpeg-turbo
           jsoncpp
           libtheora
           libx11
           libxml2
           libxt
           lz4
           mesa
           netcdf
           libpng
           proj-7
           python
           ;("pugixml" ,pugixml)
           sqlite
           libtiff
           xorgproto
           zlib))
    (propagated-inputs
     ;; VTK's 'VTK-vtk-module-find-packages.cmake' calls
     ;; 'find_package(THEORA)', which in turns looks for libogg.
     (list libogg))
    (home-page "https://vtk.org/")
    (synopsis "Libraries for 3D computer graphics")
    (description
     "The Visualization Toolkit (VTK) is a C++ library for 3D computer graphics,
image processing and visualization.  It supports a wide variety of
visualization algorithms including: scalar, vector, tensor, texture, and
volumetric methods; and advanced modeling techniques such as: implicit
modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay
triangulation.  VTK has an extensive information visualization framework, has
a suite of 3D interaction widgets, supports parallel processing, and
integrates with various databases on GUI toolkits such as Qt and Tk.")
    (license license:bsd-3)))

(define-public vtk-7
  (package
    (inherit vtk)
    (version "7.1.1")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://vtk.org/files/release/"
                                  (version-major+minor version)
                                  "/VTK-" version ".tar.gz"))
              (sha256
               (base32
                "0nm7xwwj7rnsxjdv2ssviys8nhci4n9iiiqm2y14s520hl2dsp1d"))
              (patches (search-patches "vtk-7-python-compat.patch"
                                       "vtk-7-hdf5-compat.patch"
                                       "vtk-7-gcc-10-compat.patch"))))
    (arguments
     (substitute-keyword-arguments (package-arguments vtk)
       ((#:configure-flags flags)
        ;; Otherwise, the build would fail with: "error: invalid conversion
        ;; from ‘const char*’ to ‘char*’ [-fpermissive]".
        `(cons "-DCMAKE_CXX_FLAGS=-fpermissive" ,flags))
       ((#:phases phases)
        #~(modify-phases #$phases
            (add-after 'unpack 'remove-kernel-version
              ;; Avoid embedding the kernel version for reproducible builds
              (lambda _
                (substitute*
                    "ThirdParty/hdf5/vtkhdf5/config/cmake/libhdf5.settings.cmake.in"
                  (("Host system: \\@CMAKE_HOST_SYSTEM\\@")
                   "Host system: @CMAKE_SYSTEM_NAME@"))))))))))

(define-public opencv
  (package
    (name "opencv")
    (version "4.5.4")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                     (url "https://github.com/opencv/opencv")
                     (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0gf2xs3r4s51m20mpf0wdidpk0xzp3m2w6jx72fwldhn0pshlmcj"))
              (modules '((guix build utils)))
              (snippet
               '(begin
                  ;; Remove external libraries. We have almost all available
                  ;; in Guix:
                  (with-directory-excursion "3rdparty"
                    (for-each delete-file-recursively
                              '("carotene"
                                "cpufeatures"
                                "ffmpeg"
                                "include"
                                "ippicv"
                                "ittnotify"
                                "libjasper"
                                "libjpeg"
                                "libjpeg-turbo"
                                "libpng"
                                "libtengine"
                                "libtiff"
                                "libwebp"
                                "openexr"
                                "openjpeg"
                                "openvx"
                                "protobuf"
                                ;;"quirc"
                                "tbb"
                                "zlib")))

                  ;; Milky icon set is non-free:
                  (delete-file-recursively "modules/highgui/src/files_Qt/Milky")

                  ;; Some jars found:
                  (for-each delete-file
                            '("modules/java/test/pure_test/lib/junit-4.11.jar"
                              "samples/java/sbt/sbt/sbt-launch.jar"))))))
    (build-system cmake-build-system)
    (arguments
     `(#:configure-flags
       (list "-DWITH_ADE=OFF" ;we don't have a package for ade yet
             "-DWITH_IPP=OFF"
             "-DWITH_ITT=OFF"
             "-DWITH_CAROTENE=OFF" ; only visible on arm/aarch64
             "-DENABLE_PRECOMPILED_HEADERS=OFF"
             "-DOPENCV_GENERATE_PKGCONFIG=ON"

             ;; CPU-Features:
             ;; See cmake/OpenCVCompilerOptimizations.cmake
             ;; (CPU_ALL_OPTIMIZATIONS) for a list of all optimizations
             ;; BASELINE is the minimum optimization all CPUs must support
             ;;
             ;; DISPATCH is the list of optional dispatches.
             "-DCPU_BASELINE=SSE2"

             ;; Build Python bindings.
             "-DBUILD_opencv_python3=ON"

             ,@(match (%current-system)
                 ("x86_64-linux"
                  '("-DCPU_DISPATCH=NEON;VFPV3;FP16;SSE;SSE2;SSE3;SSSE3;SSE4_1;SSE4_2;POPCNT;AVX;FP16;AVX2;FMA3;AVX_512F;AVX512_SKX"
                    "-DCPU_DISPATCH_REQUIRE=SSE3,SSSE3,SSE4_1,SSE4_2,AVX,AVX2"))
                 ("armhf-linux"
                  '("-DCPU_BASELINE_DISABLE=NEON")) ; causes build failures
                 ("aarch64-linux"
                  '("-DCPU_BASELINE=NEON"
                    "-DCPU_DISPATCH=NEON;VFPV3;FP16"))
                 (_ '()))

             "-DBUILD_PERF_TESTS=OFF"
             "-DBUILD_TESTS=ON"

             (string-append "-DOPENCV_EXTRA_MODULES_PATH=" (getcwd)
                            "/opencv-contrib/modules")

             ;;Define test data:
             (string-append "-DOPENCV_TEST_DATA_PATH=" (getcwd)
                            "/opencv-extra/testdata")

             ;; Is ON by default and would try to rebuild 3rd-party protobuf,
             ;; which we had removed, which would lead to an error:
             "-DBUILD_PROTOBUF=OFF"

             ;; Rebuild protobuf files, because we have a slightly different
             ;; version than the included one. If we would not update, we
             ;; would get a compile error later:
             "-DPROTOBUF_UPDATE_FILES=ON"

             ;; xfeatures2d disabled, because it downloads extra binaries from
             ;; https://github.com/opencv/opencv_3rdparty
             ;; defined in xfeatures2d/cmake/download_{vgg|bootdesc}.cmake
             ;; Cmp this bug entry:
             ;; https://github.com/opencv/opencv_contrib/issues/1131
             "-DBUILD_opencv_xfeatures2d=OFF")
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'disable-broken-tests
           (lambda _
             ;; This test fails with "unknown file: Failure"
             ;; But I couldn't figure out which file was missing:
             (substitute* "../opencv-contrib/modules/face/test/test_face_align.cpp"
               (("(TEST\\(CV_Face_FacemarkKazemi, )(can_detect_landmarks\\).*)"
                 all pre post)
                (string-append pre "DISABLED_" post)))

             ;; This test fails with a comparison between the expected 396 and
             ;; the actual 440 in file size.
             (substitute* "modules/imgcodecs/test/test_exr.impl.hpp"
               (("(TEST\\(Imgcodecs_EXR, )(readWrite_32FC1\\).*)" all pre post)
                (string-append pre "DISABLED_" post)))

             ;; These fail with protobuf parse errors that come from
             ;; opencv-extra/testdata.
             (substitute* "modules/dnn/test/test_layers.cpp"
               (("(TEST_P\\(Test_Caffe_layers, )\
(Accum\\).*|DataAugmentation\\).*|Resample\\).*|Correlation\\).*)" all pre post)
                (string-append pre "DISABLED_" post)))))
         (add-after 'unpack 'unpack-submodule-sources
           (lambda* (#:key inputs #:allow-other-keys)
             (mkdir "../opencv-extra")
             (mkdir "../opencv-contrib")
             (copy-recursively (assoc-ref inputs "opencv-extra")
                               "../opencv-extra")
             (copy-recursively (assoc-ref inputs "opencv-contrib")
                               "../opencv-contrib")))
         (add-after 'build 'do-not-install-3rdparty-file
           (lambda _
             (substitute* "cmake_install.cmake"
               (("file\\(INSTALL .*source/3rdparty/include/opencl/LICENSE.txt.*") "\n"))))
         (add-before 'check 'start-xserver
           (lambda* (#:key inputs #:allow-other-keys)
             (let ((xorg-server (assoc-ref inputs "xorg-server"))
                   (disp ":1"))
               (setenv "HOME" (getcwd))
               (setenv "DISPLAY" disp)
               ;; There must be a running X server and make check doesn't start one.
               ;; Therefore we must do it.
               (zero? (system (format #f "~a/bin/Xvfb ~a &" xorg-server disp)))))))))
    (native-inputs
     `(("pkg-config" ,pkg-config)
       ("xorg-server" ,xorg-server-for-tests) ; For running the tests
       ("opencv-extra"
        ,(origin
           (method git-fetch)
           (uri (git-reference
                 (url "https://github.com/opencv/opencv_extra")
                 (commit version)))
           (file-name (git-file-name "opencv_extra" version))
           (sha256
            (base32 "1fg2hxdvphdvagc2fkmhqk7qql9mp7pj2bmp8kmd7vicpr72qk82"))))
       ("opencv-contrib"
        ,(origin
           (method git-fetch)
           (uri (git-reference
                 (url "https://github.com/opencv/opencv_contrib")
                 (commit version)))
           (file-name (git-file-name "opencv_contrib" version))
           (sha256
            (base32 "0ga0l4ranp1834gxgp487ll1amvmssa02l2nk5ja5w0rx4d8hh26"))))))
    (inputs
     (list ffmpeg-4
           gtk+
           gtkglext
           hdf5
           ilmbase
           imath ;should be propagated by openexr
           jasper
           libgphoto2
           libjpeg-turbo
           libpng
           libtiff
           libwebp
           openblas
           openexr
           openjpeg
           protobuf
           python
           python-numpy
           vtk
           zlib))
    ;; These three CVEs are not a problem of OpenCV, see:
    ;; https://github.com/opencv/opencv/issues/10998
    (properties '((lint-hidden-cve . ("CVE-2018-7712"
                                      "CVE-2018-7713"
                                      "CVE-2018-7714"))))
    (synopsis "Computer vision library")
    (description "OpenCV is a library aimed at real-time computer vision,
including several hundred computer vision algorithms.  It can be used to do
things like:

@itemize
@item image and video input and output
@item image and video processing
@item displaying
@item feature recognition
@item segmentation
@item facial recognition
@item stereo vision
@item structure from motion
@item augmented reality
@item machine learning
@end itemize\n")
    (home-page "https://opencv.org/")
    (license license:bsd-3)))

(define-public vips
  (package
    (name "vips")
    (version "8.13.1")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "https://github.com/libvips/libvips/releases/download/v"
             version "/vips-" version ".tar.gz"))
       (sha256
        (base32 "00kp3439jcqv9l2gcjg88xzvlq8clv54z1m3x66i3chvarz7ndxd"))))
    (build-system gnu-build-system)
    (native-inputs
     (list gobject-introspection pkg-config))
    (inputs
     (list expat
           fftw
           giflib
           glib
           hdf5
           imagemagick
           lcms
           libexif
           libgsf
           libjpeg-turbo
           libpng
           librsvg
           libtiff
           libxml2
           libwebp
           matio
           niftilib
           openexr-2
           orc
           pango
           poppler))
    (home-page "https://libvips.github.io/libvips/")
    (synopsis "Multithreaded image processing system with low memory needs")
    (description
     "VIPS is a demand-driven, horizontally threaded image processing library.
It's particularly good at processing large images, working with colour,
scientific analysis, and general research & development.

Compared to most image processing libraries VIPS needs little RAM and runs
quickly, especially on machines with more than one CPU core.  This is primarily
due to its architecture which automatically parallelises the image workflows.")
    (license license:lgpl2.1+)))

(define-public gmic
  (package
    (name "gmic")
    (version "3.0.0")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://gmic.eu/files/source/gmic_"
                           version ".tar.gz"))
       (sha256
        (base32 "080inz0wisv3rhvbnzrgcs3j25wq86gybp68yi56gw6vwswnn19z"))))
    (build-system cmake-build-system)
    (arguments
     `(#:tests? #f ;there are no tests
       #:configure-flags '("-DBUILD_LIB_STATIC=OFF"
                           "-DENABLE_DYNAMIC_LINKING=ON"
                           "-DENABLE_LTO=ON")
       #:phases
       (modify-phases %standard-phases
         (add-before 'configure 'set-LDFLAGS
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (setenv "LDFLAGS"
                     (string-append
                      "-Wl,-rpath="
                      (assoc-ref outputs "out") "/lib")))))))
    (native-inputs
     (list pkg-config))
    (inputs
     (list curl
           fftw
           graphicsmagick
           imath
           libjpeg-turbo
           libpng
           libtiff
           libx11
           ;;opencv ;OpenCV is currently broken in the CI
           openexr
           zlib))
    (home-page "https://gmic.eu/")
    (synopsis "Full-featured framework for digital image processing")
    (description "G'MIC is a full-featured framework for digital image
processing.  It provides several user interfaces to convert / manipulate
/ filter / visualize generic image datasets, ranging from 1D scalar
signals to 3D+t sequences of multi-spectral volumetric images, hence
including 2D color images.")
    ;; Dual-licensed, either license applies.
    (license (list license:cecill license:cecill-c))))

(define-public gmic-qt
  (package
    (inherit gmic)
    (name "gmic-qt")
    (arguments
     (substitute-keyword-arguments (package-arguments gmic)
       ((#:configure-flags _)
        `(list "-DGMIC_QT_HOST=none" "-DENABLE_DYNAMIC_LINKING=ON"
               (string-append "-DGMIC_LIB_PATH="
                              (assoc-ref %build-inputs "gmic") "/lib")))
        ((#:phases phases)
         `(modify-phases ,phases
            (add-after 'unpack 'qt-chdir
              (lambda _ (chdir "gmic-qt") #t))))))
    (native-inputs
     (list pkg-config qttools-5))
    (inputs
     (modify-inputs (package-inputs gmic)
       (prepend gmic qtbase-5)))
    (synopsis "Qt frontend for the G'MIC image processing framework")
    (license license:gpl3+)))

(define-public gmic-qt-krita
  (package
    (inherit gmic-qt)
    (name "gmic-qt-krita")
    (arguments
     (substitute-keyword-arguments (package-arguments gmic-qt)
       ((#:configure-flags flags)
        '(list "-DGMIC_QT_HOST=krita" "-DENABLE_DYNAMIC_LINKING=ON"
               (string-append "-DGMIC_LIB_PATH="
                              (assoc-ref %build-inputs "gmic") "/lib")))))
    (synopsis "Krita plugin for the G'MIC image processing framework")))

(define-public gmic-qt-gimp
  (package
    (inherit gmic-qt)
    (name "gmic-qt-gimp")
    (inputs
     ;; GIMP and its dependencies.
     (modify-inputs (package-inputs gmic-qt)
       (prepend gimp gdk-pixbuf cairo gegl)))
    (arguments
     (substitute-keyword-arguments (package-arguments gmic-qt)
       ((#:configure-flags flags)
        '(list "-DGMIC_QT_HOST=gimp" "-DENABLE_DYNAMIC_LINKING=ON"
               (string-append "-DGMIC_LIB_PATH="
                              (assoc-ref %build-inputs "gmic") "/lib")))))
    (synopsis "GIMP plugin for the G'MIC image processing framework")))

(define-public nip2
  (package
    (name "nip2")
    (version "8.7.1")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://github.com/libvips/nip2/releases/download/v"
                           version "/nip2-" version ".tar.gz" ))
       (sha256
        (base32 "0l7n427njif53npqn02gfjjly8y3khbrkzqxp10j5vp9h97psgiw"))))
    (build-system gnu-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         ;; test_conv.ws keep failing so disabling for now.
         (add-after 'unpack 'disable-test-conv
           (lambda _
             (delete-file "test/workspaces/test_conv.ws")
             #t))
         (add-before 'check 'set-home
           (lambda _
             (setenv "HOME" "/tmp") #t)))))
    (inputs
     `(("vips" ,vips)
       ("glib" ,glib)
       ("libtiff" ,libtiff)
       ("gtk+-2" ,gtk+-2)
       ("libxml2" ,libxml2)
       ("libexif" ,libexif)
       ("libjpeg" ,libjpeg-turbo)        ;required by vips.pc
       ("librsvg" ,librsvg)
       ("fftw" ,fftw)
       ("libgsf" ,libgsf)
       ("imagemagick" ,imagemagick)
       ("orc" ,orc)
       ("matio" ,matio)
       ("lcms" ,lcms)
       ("libwebp" ,libwebp)
       ("openexr" ,openexr-2)
       ("poppler" ,poppler)
       ("gsl" ,gsl)))
    (native-inputs
     (list flex bison pkg-config))
    (home-page "https://github.com/libvips/nip2")
    (synopsis "Spreadsheet-like GUI for libvips")
    (description "This package provide a graphical user interface (GUI) for
the VIPS image processing library.  It's a little like a spreadsheet: you
create a set of formula connecting your objects together, and on a change nip2
recalculates.")
    (license license:gpl2+)))

;; This package bundles and extends VTK.  It also reuses the VTK build system
;; to some degree.  Sadly, it does not seem to be possible to build with an
;; external VTK, despite the CMake option PARAVIEW_USE_EXTERNAL_VTK.
(define-public paraview-5.9
  (package
    (name "paraview")
    (version "5.9.1")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://www.paraview.org/files/v"
                           (version-major+minor version)
                           "/ParaView-v" version ".tar.xz"))
       (sha256
        (base32 "13aczmfshzia324h9r2m675yyrklz2308rf98n444ppmzfv6qj0d"))))
    (build-system qt-build-system)
    (arguments
     (list
      #:build-type "Release"        ;Build without debug symbols to save space
      #:configure-flags
      '(list "-DPARAVIEW_BUILD_WITH_EXTERNAL=ON"
             "-DPARAVIEW_BUILD_SHARED_LIBS=ON"
             "-DPARAVIEW_BUILD_DEVELOPER_DOCUMENTATION=OFF"
             "-DPARAVIEW_USE_PYTHON=ON"
             "-DPARAVIEW_ENABLE_FFMPEG=ON"
             "-DPARAVIEW_ENABLE_GDAL=ON"
             "-DPARAVIEW_ENABLE_WEB=OFF"

             "-DVTK_MODULE_USE_EXTERNAL_VTK_doubleconversion=ON"
             "-DVTK_MODULE_USE_EXTERNAL_VTK_eigen=ON"
             "-DVTK_MODULE_USE_EXTERNAL_VTK_expat=ON"
             "-DVTK_MODULE_USE_EXTERNAL_VTK_freetype=ON"
             "-DVTK_MODULE_USE_EXTERNAL_VTK_gl2ps=ON"
             "-DVTK_MODULE_USE_EXTERNAL_VTK_glew=ON"
             "-DVTK_MODULE_USE_EXTERNAL_VTK_hdf5=ON"
             "-DVTK_MODULE_USE_EXTERNAL_VTK_jpeg=ON"
             "-DVTK_MODULE_USE_EXTERNAL_VTK_libxml2=ON"
             "-DVTK_MODULE_USE_EXTERNAL_VTK_lz4=ON"
             "-DVTK_MODULE_USE_EXTERNAL_VTK_lzma=ON"
             "-DVTK_MODULE_USE_EXTERNAL_VTK_netcdf=ON"
             "-DVTK_MODULE_USE_EXTERNAL_VTK_png=ON"
             "-DVTK_MODULE_USE_EXTERNAL_VTK_theora=ON"
             "-DVTK_MODULE_USE_EXTERNAL_VTK_tiff=ON"
             "-DVTK_MODULE_USE_EXTERNAL_VTK_utf8=ON"
             "-DVTK_MODULE_USE_EXTERNAL_VTK_zlib=ON"

             "-DVTK_MODULE_USE_EXTERNAL_ParaView_vtkcatalyst=OFF"
             "-DVTK_MODULE_USE_EXTERNAL_VTK_cgns=OFF"
             "-DVTK_MODULE_USE_EXTERNAL_VTK_exprtk=OFF"
             "-DVTK_MODULE_USE_EXTERNAL_VTK_fmt=OFF"
             "-DVTK_MODULE_USE_EXTERNAL_VTK_ioss=OFF")))
    (inputs
     (list ;; XXX: We can't simply #:use-module due to a cycle somewhere.
           (module-ref
            (resolve-interface '(gnu packages engineering))
            'cgns)
           cli11
           double-conversion
           eigen
           expat
           ffmpeg-4
           freetype
           gdal
           gl2ps
           glew
           hdf5
           jsoncpp
           libharu
           libjpeg-turbo
           libpng
           libtheora
           libtiff
           libxml2
           lz4
           mesa
           netcdf
           protobuf
           pugixml
           python
           qtbase-5
           qtsvg-5
           qttools-5
           qtxmlpatterns
           utfcpp
           zlib))
    (home-page "https://www.paraview.org/")
    (synopsis "Data analysis and visualization application")
    (description "ParaView is a data analysis and visualization application.
Users can quickly build visualizations to analyze their data using qualitative
and quantitative techniques.  The data exploration can be done interactively
in 3D or programmatically using ParaView’s batch processing capabilities.")
    (license license:bsd-3)))

(define-public paraview
  (package
    (name "paraview")
    (version "5.11.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://gitlab.kitware.com/paraview/paraview.git")
             (commit (string-append "v" version))
             (recursive? #t)))
       (file-name (git-file-name name version))
       (sha256
        (base32 "0qifzsbgg8f7zvg5a4934nql6nv5b6sm1f59bylyc6v5bqd0myas"))
       (modules '((guix build utils)))
       (snippet
        ;; TODO: Also remove unused bundled libraries and plugins?
        #~(begin
            ;; Remove bundled ParaView libraries which are available in Guix
            ;; or undesired.
            (for-each (lambda (dir)
                        (delete-file-recursively
                         (string-append "ThirdParty/" dir "/vtk"
                                        (string-downcase dir))))
                      '(;;"CosmoHaloFinder"
                        ;;"IceT"
                        "NvPipe"        ; Don't want NvPipe support
                        ;;"QtTesting"
                        ;;"cinema"
                        ;;"cinemasci"
                        "protobuf"))
            ;; Remove undesired ParaView plugins.
            (delete-file-recursively "Plugins/pvNVIDIAIndeX")
            ;; Remove bundled VTK libraries which are available in Guix.
            (for-each (lambda (dir)
                        (delete-file-recursively
                         (string-append "VTK/ThirdParty/" dir "/vtk" dir)))
                      '(;;"cgns"
                        "cli11"
                        ;;"diy2"
                        "doubleconversion"
                        "eigen"
                        ;;"exodusII"
                        "expat"
                        ;;"exprtk"
                        ;;"fides"
                        "fmt"
                        "freetype"
                        "gl2ps"
                        "glew"
                        ;;"h5part"
                        "hdf5"
                        ;;"ioss"
                        "jpeg"
                        "jsoncpp"
                        ;;"kissfft"
                        ;;"libharu" ; Requires some PRs applied to 2.3.0
                        "libproj"
                        "libxml2"
                        ;;"loguru"
                        "lz4"
                        "lzma"
                        "mpi4py"
                        "netcdf"
                        ;;"nlohmannjson" ; ParFlow build fails even with bundled
                        "ogg"
                        ;;"pegtl"
                        "png"
                        "pugixml"
                        "sqlite"
                        "theora"
                        "tiff"
                        "utf8"
                        ;;"verdict"
                        ;;"vpic"
                        ;;"vtkm"
                        ;;"xdmf2"
                        ;;"xdmf3"
                        ;;"zfp"
                        "zlib"))))))
    (build-system qt-build-system)
    (arguments
     (list
      #:build-type "Release"            ; 542 MiB in release mode
      #:tests? #f                       ; Downloads test data
      #:configure-flags
      #~(let ((doc (string-append #$output "/share/doc/" #$name "-" #$version)))
          (list
           (string-append "-DCMAKE_INSTALL_DOCDIR=" doc) ; For paraview.qch

           ;; ParaView build options
           "-DPARAVIEW_BUILD_DEVELOPER_DOCUMENTATION=ON"
           (string-append "-DPARAVIEW_GENERATED_DOCUMENTATION_OUTPUT_DIRECTORY=" doc)

           ;; ParaView capability options
           ;;"-DPARAVIEW_USE_EXTERNAL_VTK=ON" ; Unsupported by ParaView
           "-DPARAVIEW_USE_MPI=ON"
           "-DPARAVIEW_USE_PYTHON=ON"
           "-DPARAVIEW_USE_QTWEBENGINE=ON"

           ;; ParaView features
           ;;
           ;; Enable those that are disabled by default.
           ;; Commented means the dependencies are missing from Guix
           ;; (or are otherwise described).
           ;;"-DPARAVIEW_ENABLE_ADIOS2=ON"
           ;;"-DPARAVIEW_ENABLE_COSMOTOOLS=ON"
           ;;"-DPARAVIEW_ENABLE_CATALYST=ON"
           "-DPARAVIEW_ENABLE_FFMPEG=ON"
           ;;"-DPARAVIEW_ENABLE_FIDES=ON"
           "-DPARAVIEW_ENABLE_GDAL=ON"
           ;;"-DPARAVIEW_ENABLE_LAS=ON"
           ;;"-DPARAVIEW_ENABLE_LOOKINGGLASS=ON" ; Downloads dependency
           ;;"-DPARAVIEW_ENABLE_MOMENTINVARIANTS=ON" ; Downloads dependency
           "-DPARAVIEW_ENABLE_MOTIONFX=ON"
           ;;"-DPARAVIEW_ENABLE_OPENTURNS=ON"
           ;;"-DPARAVIEW_ENABLE_OPENVDB=ON" ; Dependency not found
           ;;"-DPARAVIEW_ENABLE_PDAL=ON"
           ;;"-DPARAVIEW_ENABLE_RAYTRACING=ON"
           "-DPARAVIEW_ENABLE_VISITBRIDGE=ON"
           "-DPARAVIEW_ENABLE_XDMF3=ON"

           ;; ParaView miscellaneous options
           ;;
           ;; Without -DPARAVIEW_DATA_EXCLUDE_FROM_ALL=OFF, test data is
           ;; downloaded even with tests disabled.
           "-DPARAVIEW_VERSIONED_INSTALL=OFF"
           "-DPARAVIEW_DATA_EXCLUDE_FROM_ALL=OFF"

           ;; ParaView plugins
           ;;
           ;; Enable those that are disabled by default.
           ;; Commented means the dependencies are missing from Guix
           ;; (or are otherwise described).
           ;;"-DPARAVIEW_PLUGIN_ENABLE_AdiosReaderPixie=ON"
           ;;"-DPARAVIEW_PLUGIN_ENABLE_AdiosReaderStaging=ON"
           "-DPARAVIEW_PLUGIN_ENABLE_CAVEInteraction=ON"
           ;;"-DPARAVIEW_PLUGIN_ENABLE_CDIReader=ON"
           "-DPARAVIEW_PLUGIN_ENABLE_GeographicalMap=ON"
           "-DPARAVIEW_PLUGIN_ENABLE_GmshIO=ON"
           "-DPARAVIEW_PLUGIN_ENABLE_InSituExodus=ON"
           ;;"-DPARAVIEW_PLUGIN_ENABLE_LookingGlass=ON"
           "-DPARAVIEW_PLUGIN_ENABLE_NetCDFTimeAnnotationPlugin=ON"
           ;;"-DPARAVIEW_PLUGIN_ENABLE_ParFlow=ON" ; Build fails
           ;;"-DPARAVIEW_PLUGIN_ENABLE_PythonQtPlugin=ON"
           "-DPARAVIEW_PLUGIN_ENABLE_SpaceMouseInteractor=ON"
           ;;"-DPARAVIEW_PLUGIN_ENABLE_VDFReaderPlugin=ON"
           ;;"-DPARAVIEW_PLUGIN_ENABLE_XRInterface=ON" ; Build fails
           ;;"-DPARAVIEW_PLUGIN_ENABLE_zSpace=ON"

           ;; VTK options
           "-DVTK_SMP_IMPLEMENTATION_TYPE=TBB"
           "-DVTKm_ENABLE_MPI=ON"

           ;; External libraries for ParaView and VTK
           "-DVTK_MODULE_USE_EXTERNAL_ParaView_protobuf=ON"
           "-DVTK_MODULE_USE_EXTERNAL_VTK_cli11=ON"
           "-DVTK_MODULE_USE_EXTERNAL_VTK_doubleconversion=ON"
           "-DVTK_MODULE_USE_EXTERNAL_VTK_eigen=ON"
           "-DVTK_MODULE_USE_EXTERNAL_VTK_expat=ON"
           "-DVTK_MODULE_USE_EXTERNAL_VTK_fmt=ON"
           "-DVTK_MODULE_USE_EXTERNAL_VTK_freetype=ON"
           "-DVTK_MODULE_USE_EXTERNAL_VTK_gl2ps=ON"
           "-DVTK_MODULE_USE_EXTERNAL_VTK_glew=ON"
           "-DVTK_MODULE_USE_EXTERNAL_VTK_hdf5=ON"
           "-DVTK_MODULE_USE_EXTERNAL_VTK_jpeg=ON"
           "-DVTK_MODULE_USE_EXTERNAL_VTK_jsoncpp=ON"
           "-DVTK_MODULE_USE_EXTERNAL_VTK_libproj=ON"
           "-DVTK_MODULE_USE_EXTERNAL_VTK_libxml2=ON"
           "-DVTK_MODULE_USE_EXTERNAL_VTK_lz4=ON"
           "-DVTK_MODULE_USE_EXTERNAL_VTK_lzma=ON"
           "-DVTK_MODULE_USE_EXTERNAL_VTK_mpi4py=ON"
           "-DVTK_MODULE_USE_EXTERNAL_VTK_netcdf=ON"
           ;;"-DVTK_MODULE_USE_EXTERNAL_VTK_nlohmannjson=ON"
           "-DVTK_MODULE_USE_EXTERNAL_VTK_ogg=ON"
           ;;"-DVTK_MODULE_USE_EXTERNAL_VTK_pegtl=ON"
           "-DVTK_MODULE_USE_EXTERNAL_VTK_png=ON"
           "-DVTK_MODULE_USE_EXTERNAL_VTK_pugixml=ON"
           "-DVTK_MODULE_USE_EXTERNAL_VTK_sqlite=ON"
           "-DVTK_MODULE_USE_EXTERNAL_VTK_theora=ON"
           "-DVTK_MODULE_USE_EXTERNAL_VTK_tiff=ON"
           "-DVTK_MODULE_USE_EXTERNAL_VTK_utf8=ON"
           "-DVTK_MODULE_USE_EXTERNAL_VTK_zlib=ON"))
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'set-paths 'hide-gfortran
            (lambda _
              (setenv "CPLUS_INCLUDE_PATH"
                      (string-join
                       (delete (string-append #$(this-package-native-input "gfortran")
                                              "/include/c++")
                               (string-split (getenv "CPLUS_INCLUDE_PATH") #\:))
                       ":"))))
          (replace 'install-license-files
            (lambda _
              (let ((src (string-append #$output "/share/licenses/ParaView"))
                    (dst (string-append #$output "/share/doc/"
                                        #$name "-" #$version "/licenses")))
                (copy-recursively src dst)
                (delete-file-recursively (dirname src))))))))
    (native-inputs
     (list gfortran
           ;; For the documentation
           doxygen
           graphviz
           perl
           python-sphinx))
    (inputs
     (list boost
           cli11
           curl
           double-conversion
           eigen
           expat
           ffmpeg
           fmt
           freetype
           gdal
           gl2ps
           glew
           gmsh
           hdf5
           ;;json-modern-cxx              ;For ParFlow; build fails
           jsoncpp
           libjpeg-turbo
           libogg
           libpng
           libtheora
           libtiff
           libxcursor
           libxml2
           libxt
           lz4
           lzip
           mesa
           netcdf
           openmpi
           ;;openvdb                      ;For OpenVDB; dependency not found
           ;;openvr                       ;For XRInterface; build fails
           ;;pegtl                        ;For VTK; build fails
           proj
           protobuf
           pugixml
           python-cftime
           python-matplotlib
           python-mpi4py
           python-numpy
           python-wrapper
           qtbase-5
           qtdeclarative-5
           qtmultimedia-5
           qtsvg-5
           qttools-5
           qtwebchannel-5
           qtwebengine-5
           qtx11extras
           qtxmlpatterns
           sdl2
           sqlite
           tbb
           utfcpp
           zlib))
    (home-page "https://www.paraview.org/")
    (synopsis "VTK-based, parallel data analyzer and visualizer")
    (description "ParaView is a VTK-based, parallel data analyzer and
visualizer which allows exploring data interactively in 3D or
programmatically.")
    (license license:bsd-3)))

(define-public vxl
  (package
    (name "vxl")
    (version "2.0.2")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/vxl/vxl")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "0949hw57szq8943f1whwqaz591xjmb19kj803hcv74hdai2b0ycg"))
       (modules '((guix build utils)))
       ;; TODO: vxl includes an old version of dcmtk.  It won't build with
       ;; version 3.6.x.
       (snippet
        '(begin
           (for-each delete-file-recursively
                     '("v3p/bzlib/"
                       "v3p/geotiff/"
                       "v3p/jpeg/"
                       "v3p/png/"
                       "v3p/tiff/"
                       "v3p/zlib/"))
           (substitute* "v3p/CMakeLists.txt"
             (("add_subdirectory\\((tiff|png|jpeg|zlib|bzlib|geotiff)\\)")
              ""))
           #t))))
    (build-system cmake-build-system)
    (inputs
     (list libgeotiff libtiff libjpeg-turbo libpng zlib))
    (home-page "https://github.com/vxl/vxl/")
    (synopsis "Collection of C++ libraries for computer vision")
    (description "VXL (the Vision-something-Libraries) is a collection of C++
libraries designed for computer vision research and implementation.")
    (license license:bsd-3)))

(define-public vxl-1
  (package (inherit vxl)
    (name "vxl")
    (version "1.18.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/vxl/vxl")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "1g4mr2cc58jwm0vasscbd4y5380wj3ahkvq121z4gs83fhavvxgz"))
       (modules '((guix build utils)))
       (snippet
        '(begin
           (for-each delete-file-recursively
                     '("v3p/bzlib/"
                       "v3p/geotiff/"
                       "v3p/png/"
                       "v3p/tiff/"
                       "v3p/zlib/"))
           (substitute* "v3p/CMakeLists.txt"
             (("add_subdirectory\\((tiff|png|jpeg|zlib|bzlib|geotiff)\\)")
              ""))
           #t))))
    (arguments
     `(#:configure-flags
       ;; Needed for itk-snap
       (list "-DVNL_CONFIG_LEGACY_METHODS=ON")))))

(define-public insight-toolkit
  (package
    (name "insight-toolkit")
    (version "5.0.0")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://github.com/InsightSoftwareConsortium/ITK/"
                           "releases/download/v" version "/InsightToolkit-"
                           version ".tar.xz"))
       (sha256
        (base32 "0bs63mk4q8jmx38f031jy5w5n9yy5ng9x8ijwinvjyvas8cichqi"))))
    (build-system cmake-build-system)
    (arguments
     `(#:tests? #f            ; tests require network access and external data
       #:configure-flags
       '("-DITK_USE_GPU=ON"
         "-DITK_USE_SYSTEM_LIBRARIES=ON"
         "-DITK_USE_SYSTEM_GOOGLETEST=ON"
         "-DITK_BUILD_SHARED=ON"
         ;; This prevents "GTest::GTest" from being added to the ITK_LIBRARIES
         ;; variable in the installed CMake files.  This is necessary as other
         ;; packages using insight-toolkit could not be configured otherwise.
         "-DGTEST_ROOT=gtest")

       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'do-not-tune
           (lambda _
             (substitute* "CMake/ITKSetStandardCompilerFlags.cmake"
               (("-mute=native") ""))
             #t)))))
    (inputs
     `(("eigen" ,eigen)
       ("expat" ,expat)
       ("fftw" ,fftw)
       ("fftwf" ,fftwf)
       ("hdf5" ,hdf5)
       ("libjpeg" ,libjpeg-turbo)
       ("libpng" ,libpng)
       ("libtiff" ,libtiff)
       ("mesa" ,mesa-opencl)
       ("perl" ,perl)
       ("python" ,python)
       ("tbb" ,tbb)
       ("vxl" ,vxl-1)
       ("zlib" ,zlib)))
    (native-inputs
     (list googletest pkg-config))
    (home-page "https://github.com/InsightSoftwareConsortium/ITK/")
    (synopsis "Scientific image processing, segmentation and registration")
    (description "The Insight Toolkit (ITK) is a toolkit for N-dimensional
scientific image processing, segmentation, and registration.  Segmentation is
the process of identifying and classifying data found in a digitally sampled
representation.  Typically the sampled representation is an image acquired
from such medical instrumentation as CT or MRI scanners.  Registration is the
task of aligning or developing correspondences between data.  For example, in
the medical environment, a CT scan may be aligned with a MRI scan in order to
combine the information contained in both.")
    (license license:asl2.0)))

(define-public insight-toolkit-4
  (package (inherit insight-toolkit)
    (version "4.13.2")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://github.com/InsightSoftwareConsortium/ITK/"
                           "releases/download/v" version "/InsightToolkit-"
                           version ".tar.xz"))
       (sha256
        (base32 "19cgfpd63gqrvc3m27m394gy2d7w79g5y6lvznb5qqr49lihbgns"))))
    (arguments
     `(#:tests? #f            ; tests require network access and external data
       #:configure-flags
       '("-DITKV3_COMPATIBILITY=ON"     ; needed for itk-snap
         "-DITK_USE_GPU=ON"
         "-DITK_USE_SYSTEM_LIBRARIES=ON"
         "-DITK_USE_SYSTEM_GOOGLETEST=ON"
         "-DITK_USE_SYSTEM_VXL=ON")))))

(define-public insight-toolkit-4.12
  (package (inherit insight-toolkit-4)
    (version "4.12.2")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "mirror://sourceforge/itk/itk/4.12/"
                           "InsightToolkit-" version ".tar.xz"))
       (sha256
        (base32 "1qw9mxbh083siljygahl4gdfv91xvfd8hfl7ghwii19f60xrvn2w"))))))

(define-public itk-snap
  (package
    (name "itk-snap")
    (version "3.8.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://git.code.sf.net/p/itk-snap/src")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "15i5ixpryfrbf3vrrb5rici8fb585f25k0v1ljds16bp1f1msr4q"))
       (patches (search-patches "itk-snap-alt-glibc-compat.patch"))))
    (build-system cmake-build-system)
    (arguments
     `(#:configure-flags
       (list "-DSNAP_VERSION_GIT_SHA1=release"
             "-DSNAP_VERSION_GIT_BRANCH=release"
             "-DSNAP_VERSION_GIT_TIMESTAMP=0"
             "-DSNAP_PACKAGE_QT_PLUGINS=OFF"
             "-DCMAKE_POSITION_INDEPENDENT_CODE=ON")
       #:phases
       (modify-phases %standard-phases
         ;; During the installation phase all libraries provided by all
         ;; dependencies will be copied to the lib directory.  That's insane,
         ;; so we disable this.
         (add-after 'unpack 'do-not-copy-dependencies
           (lambda _
             (substitute* "CMakeLists.txt"
               (("install_qt5_executable\
\\(\\$\\{SNAP_MAIN_INSTALL_DIR\\}/\\$\\{SNAP_EXE\\}\\)")
                ""))))
         (add-after 'unpack 'disable-gui-tests
           (lambda _
             ;; The GUI tests just time out.
             (substitute* "CMakeLists.txt"
               (("  (Workspace|DiffSpace|ProbeIntensity|RegionCompetition\
|RandomForest|RandomForestBailOut)")
                ""))))
         (add-after 'unpack 'make-reproducible
           (lambda _
             (substitute* "CMakeLists.txt"
               (("TODAY\\(SNAP_VERSION_COMPILE_DATE\\)")
                "SET(SNAP_VERSION_COMPILE_DATE \"(removed for reproducibility)\")"))))
         (add-after 'unpack 'prepare-submodules
           (lambda* (#:key inputs #:allow-other-keys)
             (rmdir "Submodules/c3d")
             (copy-recursively (assoc-ref inputs "c3d-src")
                               "Submodules/c3d")
             (substitute* '("Submodules/c3d/adapters/BiasFieldCorrectionN4.cxx"
                            "Submodules/c3d/adapters/ApplyMetric.cxx")
               (("vcl_") "std::"))
             (rmdir "Submodules/greedy")
             (symlink (assoc-ref inputs "greedy-src")
                      "Submodules/greedy")))
         (add-after 'unpack 'fix-includes
           (lambda _
             (substitute* "GUI/Model/RegistrationModel.cxx"
               (("<vnl_symmetric_eigensystem.h>")
                "<vnl/algo/vnl_symmetric_eigensystem.h>"))))
         (add-before 'check 'prepare-tests
           (lambda _
             ;; Needed by at least one test.
             (setenv "HOME" "/tmp")))
         (add-after 'install 'wrap-executable
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (let ((out (assoc-ref outputs "out")))
               (wrap-program (string-append out "/bin/itksnap")
                 `("QT_PLUGIN_PATH" ":" prefix
                   ,(map (lambda (label)
                           (string-append (assoc-ref inputs label)
                                          "/lib/qt5/plugins"))
                         '("qtbase" "qtdeclarative-5"))))))))))
    (inputs
     (list curl
           fftw
           fftwf
           glu
           hdf5
           mesa-opencl
           ;; This package does not build with either insight-toolkit 5.0.0
           ;; and not with 4.13.  It really needs to be 4.12.
           insight-toolkit-4.12
           vtk-7
           qtbase-5
           qtdeclarative-5
           vxl-1
           zlib))
    (native-inputs
     `(("googletest" ,googletest)
       ("qttools-5" ,qttools-5)
       ("pkg-config" ,pkg-config)
       ("c3d-src"
        ,(let* ((commit "f521358db26e00002c911cc47bf463b043942ad3")
                (revision "1")
                (version (git-version "0" revision commit)))
           (origin
             (method git-fetch)
             (uri (git-reference
                   (url "https://github.com/pyushkevich/c3d")
                   (commit commit)))
             (file-name (git-file-name "c3d" version))
             (sha256
              (base32
               "0kyv3rxrxwr8c3sa9zv01lsnhk95b27gx1s870k3yi8qp52h7bx3")))))
       ;; We are using an arbitrary commit from 2017 because the latest
       ;; version breaks the build...
       ("greedy-src"
        ,(let* ((commit "97e340f7e8e66597599144947775e6039e79a0d3")
                (revision "1")
                (version (git-version "0" revision commit)))
           (origin
             (method git-fetch)
             (uri (git-reference
                   (url "https://github.com/pyushkevich/greedy")
                   (commit commit)))
             (file-name (git-file-name "greedy" version))
             (sha256
              (base32
               "0k5bc9za4jrc8z9dj08z1rkcp5xf0gnd1d2jmi1w9ny4vxh2q2ab")))))))
    (home-page "https://sourceforge.net/p/itk-snap/")
    (synopsis "Medical image segmentation")
    (description "ITK-SNAP is a tool for segmenting anatomical structures in
medical images.  It provides an automatic active contour segmentation
pipeline, along with supporting a manual segmentation toolbox.  ITK-SNAP has a
full-featured UI aimed at clinical researchers.")
    ;; This includes the submodules greedy and c3d.
    (license license:gpl3+)))

(define-public metapixel
  ;; Follow stable branch.
  (let ((commit "98ee9daa093b6c334941242e63f90b1c2876eb4f"))
    (package
      (name "metapixel")
      (version (git-version "1.0.2" "1" commit))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/schani/metapixel")
               (commit commit)
               ;; TODO: Package rwimg and lispreader?
               (recursive? #t)))
         (file-name (git-file-name name version))
         (sha256
          (base32 "0r7n3a6bvcxkbpda4mwmrpicii09iql5z69nkjqygkwxw7ny3309"))))
      (build-system gnu-build-system)
      (inputs
       `(("giflib" ,giflib)
         ("libjpeg" ,libjpeg-turbo)
         ("libpng" ,libpng)
         ("perl" ,perl)))
      (native-inputs
       `(("pkg-config" ,pkg-config)
         ("docbook-xml" ,docbook-xml)
         ("docbook-xsl" ,docbook-xsl)
         ("xsltproc" ,libxslt)))
      (arguments
       `(#:tests? #f                    ; No tests.
         #:make-flags (list
                       (string-append "PREFIX=" (assoc-ref %outputs "out"))
                       (string-append "MANPAGE_XSL="
                                      (assoc-ref %build-inputs "docbook-xsl")
                                      "/xml/xsl/docbook-xsl-*/manpages/docbook.xsl"))
         #:phases
         (modify-phases %standard-phases
           (delete 'configure)
           (add-before 'install 'make-local-docbook-xml
             (lambda* (#:key inputs #:allow-other-keys)
               (substitute* "metapixel.xml"
                 (("http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd")
                  (string-append (assoc-ref inputs "docbook-xml")
                                 "/xml/dtd/docbook/docbookx.dtd")))
               #t))
           (add-before 'install 'fix-directory-creation
             (lambda* (#:key outputs #:allow-other-keys)
               (mkdir-p (string-append (assoc-ref outputs "out") "/share/man/man1"))
               #t)))))
      (home-page "https://www.complang.tuwien.ac.at/schani/metapixel/")
      (synopsis "Photomosaics generator")
      (description "Metapixel is a program for generating photomosaics.  It can
generate classical photomosaics, in which the source image is viewed as a
matrix of equally sized rectangles for each of which a matching image is
substituted, as well as collage-style photomosaics, in which rectangular parts
of the source image at arbitrary positions (i.e. not aligned to a matrix) are
substituted by matching images.")
      (license license:gpl2))))

(define-public scantailor-advanced
  (let ((commit "3d1e74e6ace413733511086934a66f4e3f7a6027"))
    (package
      (name "scantailor-advanced")
      (version (string-append "1.0.16-" (string-take commit 7)))
      (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/4lex4/scantailor-advanced")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
          (base32
           "0kixwjb2x457dq7927hkh34c803p7yh1pmn6n61rk9shqrcg492h"))))
      (build-system qt-build-system)
      (native-inputs
       (list qttools-5))
      (inputs
       `(("boost" ,boost)
         ("libjpeg" ,libjpeg-turbo)
         ("libpng" ,libpng)
         ("libtiff" ,libtiff)
         ("qtbase" ,qtbase-5)
         ("qtsvg-5" ,qtsvg-5)
         ("zlib" ,zlib)))
      (arguments
       `(#:phases
         (modify-phases %standard-phases
           ;; Some tests require a display and fail with offscreen mode.
           (add-after 'unpack 'disable-failing-tests
             (lambda _
               (setenv "ARGS" "--exclude-regex \"imageproc_.*\"")
               #t)))))
      (home-page "https://github.com/4lex4/scantailor-advanced")
      (synopsis "Clean up scanned pages")
      (description "Scan Tailor is an interactive post-processing tool for
scanned pages.  It performs operations such as page splitting, deskewing,
adding/removing borders, and others.  You give it raw scans, and you get pages
ready to be printed or assembled into a PDF or DJVU file.  Scanning, optical
character recognition, and assembling multi-page documents are out of scope of
this project.

Scan Tailer Advanced is a fork of Scan Tailer that merges Scan Tailor Featured
and Scan Tailor Enhanced versions as well as including many more bug fixes.")
      (license license:gpl3+))))

(define-public stiff
  (package
    (name "stiff")
    (version "2.4.0")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://www.astromatic.net/download/stiff/stiff-"
                           version ".tar.gz"))
       (sha256
        (base32 "14m92dskzw7bwsr64ha4p0mj3ndv13gwcbfic3qxrs3zq5353s7l"))))
    (build-system gnu-build-system)
    (inputs
     (list libtiff zlib libjpeg-turbo))
    (home-page "https://www.astromatic.net/software/stiff")
    (synopsis "Convert scientific FITS images to TIFF format")
    (description
     "STIFF is a program that converts scientific @acronym{FITS, Flexible Image
Transport System} images to the more popular TIFF format for illustration
purposes.")
    (license license:gpl3+)))

(define-public python-imgviz
  (package
    (name "python-imgviz")
    (version "1.2.6")
    (source
     (origin
       ;; PyPi tarball lacks tests.
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/wkentaro/imgviz.git")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "1bm0wdv5p26i8nl4kx3145cz553v401sgbpgc96sddzjfmfiydcw"))))
    (build-system python-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (replace 'check
           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
             (when tests?
               (add-installed-pythonpath inputs outputs)
               (invoke "pytest" "-v" "tests"))
             #t)))))
    (propagated-inputs
      (list python-matplotlib python-numpy python-pillow python-pyyaml))
    (native-inputs (list python-pytest))
    (home-page "http://github.com/wkentaro/imgviz")
    (synopsis "Image Visualization Tools")
    (description "Python library for object detection, semantic and instance
segmentation.")
    (license license:expat)))

(define-public labelme
  (package
    (name "labelme")
    (version "4.5.13")
    (source
     (origin
       ;; PyPi tarball lacks tests.
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/wkentaro/labelme.git")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "0cmi2xb4dgh7738l259rgwhn9l134f0vnaaqc2gflc5yr3lqhrv2"))))
    (build-system python-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'loosen-requirements
           (lambda _
             ;; Don't require an outdated version of matplotlib.
             (substitute* "setup.py"
               (("matplotlib<3\\.3")
                "matplotlib"))))
         (add-before 'check 'start-xserver
           (lambda* (#:key inputs #:allow-other-keys)
             (let ((xorg-server (assoc-ref inputs "xorg-server")))
               ;; Options taken from CI workflow.
               (system (string-append xorg-server "/bin/Xvfb :99 -screen 0 "
                                      "1920x1200x24 -ac +extension GLX +render "
                                      "-noreset &"))
               (setenv "DISPLAY" ":99.0"))))
         (replace 'check
           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
             (when tests?
               (add-installed-pythonpath inputs outputs)
               ;; Fails when invoking help2man for unknown reason.
               (delete-file "tests/docs_tests/man_tests/test_labelme_1.py")
               ;; One test hangs.
               (delete-file "tests/labelme_tests/widgets_tests/test_label_dialog.py")
               ;; Calls incompatible function signatures.
               (delete-file "tests/labelme_tests/widgets_tests/test_label_list_widget.py")
               (setenv "MPLBACKEND" "agg")
               (invoke "pytest" "-v" "tests" "-m" "not gpu")))))))
    (propagated-inputs
      (list python-imgviz
            python-matplotlib
            python-numpy
            python-pillow
            python-pyyaml
            python-qtpy
            python-termcolor))
    (native-inputs
      (list python-pytest python-pytest-qt xorg-server-for-tests))
    (home-page "https://github.com/wkentaro/labelme")
    (synopsis
      "Image Polygonal Annotation")
    (description
      "Image and video labeling tool supporting different shapes like
polygons, rectangles, circles, lines, points and VOC/COCO export.")
    (license license:gpl3+)))

(define-public charls
  (package
    (name "charls")
    (version "2.3.4")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/team-charls/charls/")
                    (commit (string-append version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0g3f1rfimk30rqmi7ic4i5vfphyqbbpsyyhwqq1iss9wjwaz2vs5"))))
    (build-system cmake-build-system)
    (arguments
     `(#:configure-flags '("-DCMAKE_BUILD_TYPE:STRING=Release"
                           "-DBUILD_SHARED_LIBS=On")))
    (native-inputs (list git pkg-config))
    (home-page "https://github.com/team-charls/charls")
    (synopsis "Library for using JPEG-LS compliant images")
    (description
     "CharLS is a codec library that can be used to build applications that
can handle JPEG-LS compliant images.  In the application you are writing you
can call the CharLS codec and pass it images (sometimes called raster bitmaps),
 to have them encoded to JPEG-LS, or JPEG-LS streams, which CharLS will decode
to images.")
    (license license:bsd-3)))