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guix/gnu/packages/image-processing.scm
Marius Bakke 8f8bc40677
gnu: VTK: Update to 8.2.0. 
* gnu/packages/image-processing.scm (vtk): Update to 8.2.0.
2019-01-31 20:57:21 +01:00

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;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2017 John Darrington <jmd@gnu.org>
;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2014 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2014 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
;;; Copyright © 2018 Lprndn <guix@lprndn.info>
;;; Copyright © 2019 Efraim Flashner <efraim@flashner.co.il>
;;;
;;; 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 utils)
#:use-module (guix download)
#:use-module (guix git-download)
#:use-module (guix build-system cmake)
#:use-module (guix build-system gnu)
#:use-module (gnu packages)
#:use-module (gnu packages algebra)
#:use-module (gnu packages bison)
#:use-module (gnu packages boost)
#:use-module (gnu packages compression)
#:use-module (gnu packages documentation)
#:use-module (gnu packages flex)
#:use-module (gnu packages fontutils)
#:use-module (gnu packages ghostscript)
#: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 image)
#:use-module (gnu packages imagemagick)
#:use-module (gnu packages maths)
#: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 protobuf)
#:use-module (gnu packages python)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages serialization)
#: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))
;; We use the latest snapshot of this package because the latest release is
;; from 2011 and has known vulnerabilities that cannot easily be fixed by
;; applying patches.
(define-public dcmtk
(package
(name "dcmtk")
(version "3.6.1_20170228")
(source (origin
(method url-fetch)
(uri (string-append "ftp://dicom.offis.de/pub/dicom/offis/"
"software/dcmtk/snapshot/dcmtk-"
version ".tar.gz"))
(sha256
(base32
"04cwfx8yrscqcd59mxk2fh6314ckayi9cp68iql5a57pf2pg5qld"))))
(build-system gnu-build-system)
(inputs
`(("libtiff" ,libtiff)
("libpng" ,libpng)
("doxygen" ,doxygen)
("zlib" ,zlib)))
(native-inputs
`(("perl" ,perl)))
(home-page "http://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 "2.4.6")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/mia/mia/"
(version-major+minor version)
"/mia-" version ".tar.xz"))
(sha256
(base32
"0j4nd5z7i3v199jh7hqqhwd4g7snchizkc7rhzanpvngqg91m1pb"))))
(build-system cmake-build-system)
(arguments
`(#:configure-flags
(list "-DMIA_CREATE_NIPYPE_INTERFACES=0"
"-DCMAKE_CXX_FLAGS=-fpermissive")))
(inputs
`(("boost" ,boost)
("dcmtk" ,dcmtk)
("doxygen" ,doxygen)
("eigen" ,eigen)
("fftw" ,fftw)
("fftwf" ,fftwf)
("gsl" ,gsl)
("gts" ,gts)
("hdf5" ,hdf5)
("itpp" ,itpp)
("libjpeg" ,libjpeg)
("libpng" ,libpng)
("libtiff" ,libtiff)
("libxml" ,libxml2)
("libxml++" ,libxml++)
("maxflow" ,maxflow)
("niftilib" ,niftilib)
("nlopt" ,nlopt)
("openexr" ,openexr)
("python-lxml" ,python2-lxml)
("vtk" ,vtk)))
(native-inputs
`(("pkg-config" ,pkg-config)
("python" ,python-2)))
(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 vtk
(package
(name "vtk")
(version "8.2.0")
(source (origin
(method url-fetch)
(uri (string-append "https://vtk.org/files/release/"
(version-major+minor version)
"/VTK-" version ".tar.gz"))
(sha256
(base32
"1fspgp8k0myr6p2a6wkc21ldcswb4bvmb484m12mxgk1a9vxrhrl"))))
(build-system cmake-build-system)
(arguments
'(#:build-type "Release" ;Build without '-g' to save space.
;; -DVTK_USE_SYSTEM_NETCDF:BOOL=TRUE requires netcdf_cxx
#:configure-flags '("-DVTK_USE_SYSTEM_EXPAT:BOOL=TRUE"
"-DVTK_USE_SYSTEM_FREETYPE:BOOL=TRUE"
"-DVTK_USE_SYSTEM_HDF5:BOOL=TRUE"
"-DVTK_USE_SYSTEM_JPEG:BOOL=TRUE"
"-DVTK_USE_SYSTEM_JSONCPP:BOOL=TRUE"
"-DVTK_USE_SYSTEM_LIBXML2:BOOL=TRUE"
"-DVTK_USE_SYSTEM_OGGTHEORA:BOOL=TRUE"
"-DVTK_USE_SYSTEM_PNG:BOOL=TRUE"
"-DVTK_USE_SYSTEM_TIFF:BOOL=TRUE"
"-DVTK_USE_SYSTEM_ZLIB:BOOL=TRUE")
#:tests? #f)) ;XXX: no "test" target
(inputs
`(("libXt" ,libxt)
("xorgproto" ,xorgproto)
("libX11" ,libx11)
("libxml2" ,libxml2)
("mesa" ,mesa)
("glu" ,glu)
("expat" ,expat)
("freetype" ,freetype)
("hdf5" ,hdf5)
("jpeg" ,libjpeg)
("jsoncpp" ,jsoncpp)
("libogg" ,libogg)
("libtheora" ,libtheora)
("png" ,libpng)
("tiff" ,libtiff)
("zlib" ,zlib)))
(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 opencv
(package
(name "opencv")
(version "3.4.3")
(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
"06bc61r8myym4s8im10brdjfg4wxkrvsbhhl7vr1msdan2xddzi3"))
(modules '((guix build utils)))
(snippet
'(begin
;; Remove external libraries. We have all available in Guix:
(delete-file-recursively "3rdparty")
;; 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"))
#t))))
(build-system cmake-build-system)
(arguments
`(#:configure-flags
(list "-DWITH_IPP=OFF"
"-DWITH_ITT=OFF"
"-DWITH_CAROTENE=OFF" ; only visible on arm/aarch64
"-DENABLE_PRECOMPILED_HEADERS=OFF"
;; 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"
,@(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 _
;; These tests fails with:
;; vtkXOpenGLRenderWindow (0x723990): Could not find a decent config
;; I think we have no OpenGL support with the Xvfb.
(substitute* '("modules/viz/test/test_tutorial3.cpp"
"modules/viz/test/test_main.cpp"
"modules/viz/test/tests_simple.cpp"
"modules/viz/test/test_viz3d.cpp")
(("(TEST\\(Viz, )([a-z].*\\).*)" all pre post)
(string-append pre "DISABLED_" post)))
;; This one 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)))
;; Failure reason: Bad accuracy
;; Incorrect count of accurate poses [2nd case]: 90.000000 / 94.000000
(substitute* "../opencv-contrib/modules/rgbd/test/test_odometry.cpp"
(("(TEST\\(RGBD_Odometry_Rgbd, )(algorithmic\\).*)" all pre post)
(string-append pre "DISABLED_" post)))
#t))
(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")
(invoke "tar" "xvf"
(assoc-ref inputs "opencv-contrib")
"--strip-components=1"
"-C" "../opencv-contrib")))
(add-after 'set-paths 'add-ilmbase-include-path
(lambda* (#:key inputs #:allow-other-keys)
;; OpenEXR propagates ilmbase, but its include files do not appear
;; in the CPATH, so we need to add "$ilmbase/include/OpenEXR/" to
;; the CPATH to satisfy the dependency on "ImathVec.h".
(setenv "CPATH"
(string-append (assoc-ref inputs "ilmbase")
"/include/OpenEXR"
":" (or (getenv "CPATH") "")))
#t))
(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 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 "08p5xnq8n1jw8svvz0fnirfg7q8dm3p4a5dl7527s5xj0f9qn7lp"))))
("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))
(patches (search-patches "opencv-rgbd-aarch64-test-fix.patch"))
(sha256
(base32 "1f334glf39nk42mpqq6j732h3ql2mpz89jd4mcl678s8n73nfjh2"))))))
(inputs `(("libjpeg" ,libjpeg)
("libpng" ,libpng)
("jasper" ,jasper)
;; ffmpeg 4.0 causes core dumps in tests.
("ffmpeg" ,ffmpeg-3.4)
("libtiff" ,libtiff)
("hdf5" ,hdf5)
("libgphoto2" ,libgphoto2)
("libwebp" ,libwebp)
("zlib" ,zlib)
("gtkglext" ,gtkglext)
("openexr" ,openexr)
("ilmbase" ,ilmbase)
("gtk+" ,gtk+-2)
("python-numpy" ,python-numpy)
("protobuf" ,protobuf)
("vtk" ,vtk)
("python" ,python)))
;; 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 "8.7.1")
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/libvips/libvips/releases/download/v"
version "/vips-" version ".tar.gz"))
(sha256
(base32 "1w3b90pdw7nj2p0gb4f96h6zhmga513f968ldfhz1rkhg7y81c0s"))))
(build-system gnu-build-system)
(native-inputs
`(("pkg-config" ,pkg-config)
("gobject-introspection" ,gobject-introspection)))
(inputs
`(("glib" ,glib)
("libjpeg" ,libjpeg)
("libpng" ,libpng)
("librsvg" ,librsvg)
("libtiff" ,libtiff)
("libexif" ,libexif)
("giflib" ,giflib)
("libgsf" ,libgsf)
("fftw" ,fftw)
("poppler" ,poppler)
("pango" ,pango)
("lcms" ,lcms)
("matio" ,matio)
("libwebp" ,libwebp)
("niftilib" ,niftilib)
("openexr" ,openexr)
("orc" ,orc)
("imagemagick" ,imagemagick)
("libxml2" ,libxml2)
("expat" ,expat)
("hdf5" ,hdf5)))
(home-page "https://libvips.github.io/libvips/")
(synopsis "Image processing system")
(description
"vips is a demand-driven, horizontally threaded image processing library.")
(license license:lgpl2.1+)))
(define-public nip2
(package
(name "nip2")
(version "8.7.0")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/libvips/nip2/releases/download/v"
version "/nip2-" version ".tar.gz" ))
(sha256
(base32 "08dxfds4n1vxdilxcw01741a2r6fxyhawi656b7f0hy6znnkbsbc"))))
(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) ;required by vips.pc
("librsvg" ,librsvg)
("fftw" ,fftw)
("libgsf" ,libgsf)
("imagemagick" ,imagemagick)
("orc" ,orc)
("matio" ,matio)
("lcms" ,lcms)
("libwebp" ,libwebp)
("openexr" ,openexr)
("poppler" ,poppler)
("gsl" ,gsl)))
(native-inputs
`(("flex" ,flex)
("bison" ,bison)
("pkg-config" ,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+)))
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