843 lines
32 KiB
Scheme
843 lines
32 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2017 John Darrington <jmd@gnu.org>
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;;; Copyright © 2017, 2019 Ricardo Wurmus <rekado@elephly.net>
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;;; Copyright © 2014 Ludovic Courtès <ludo@gnu.org>
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;;; Copyright © 2014 Mark H Weaver <mhw@netris.org>
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;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.org>
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;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
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;;; Copyright © 2018 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
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;;; Copyright © 2018 Lprndn <guix@lprndn.info>
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;;; Copyright © 2019 Efraim Flashner <efraim@flashner.co.il>
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;;;
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;;; This file is part of GNU Guix.
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;;;
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;;; GNU Guix is free software; you can redistribute it and/or modify it
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;;; under the terms of the GNU General Public License as published by
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;;; the Free Software Foundation; either version 3 of the License, or (at
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;;; your option) any later version.
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;;;
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;;; GNU Guix is distributed in the hope that it will be useful, but
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;;; WITHOUT ANY WARRANTY; without even the implied warranty of
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;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;;; GNU General Public License for more details.
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;;;
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;;; You should have received a copy of the GNU General Public License
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;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
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(define-module (gnu packages image-processing)
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#:use-module ((guix licenses) #:prefix license:)
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#:use-module (guix packages)
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#:use-module (guix utils)
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#:use-module (guix download)
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#:use-module (guix git-download)
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#:use-module (guix build-system cmake)
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#:use-module (guix build-system gnu)
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#:use-module (gnu packages)
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#:use-module (gnu packages algebra)
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#:use-module (gnu packages bison)
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#:use-module (gnu packages boost)
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#:use-module (gnu packages check)
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#:use-module (gnu packages compression)
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#:use-module (gnu packages curl)
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#:use-module (gnu packages documentation)
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#:use-module (gnu packages flex)
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#:use-module (gnu packages fontutils)
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#:use-module (gnu packages geo)
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#:use-module (gnu packages ghostscript)
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#:use-module (gnu packages gl)
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#:use-module (gnu packages glib)
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#:use-module (gnu packages gnome)
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#:use-module (gnu packages graphics)
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#:use-module (gnu packages graphviz)
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#:use-module (gnu packages gstreamer)
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#:use-module (gnu packages gtk)
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#:use-module (gnu packages image)
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#:use-module (gnu packages imagemagick)
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#:use-module (gnu packages maths)
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#:use-module (gnu packages pdf)
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#:use-module (gnu packages perl)
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#:use-module (gnu packages photo)
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#:use-module (gnu packages pkg-config)
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#:use-module (gnu packages protobuf)
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#:use-module (gnu packages python)
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#:use-module (gnu packages python-xyz)
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#:use-module (gnu packages qt)
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#:use-module (gnu packages serialization)
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#:use-module (gnu packages tbb)
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#:use-module (gnu packages tls)
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#:use-module (gnu packages video)
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#:use-module (gnu packages xiph)
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#:use-module (gnu packages xml)
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#:use-module (gnu packages xorg)
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#:use-module (ice-9 match)
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#:use-module (srfi srfi-1))
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(define-public dcmtk
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(package
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(name "dcmtk")
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(version "3.6.4")
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(source
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(origin
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(method url-fetch)
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(uri
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(string-append "ftp://dicom.offis.de/pub/dicom/offis/software/dcmtk/"
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"dcmtk" (string-join (string-split version #\.) "")
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"/dcmtk-" version ".tar.gz"))
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(sha256
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(base32 "1h22z8g0kmvhg8lgkbikyzyphhvxvq6018a00yd6i4g0z9ag6gx9"))))
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(build-system cmake-build-system)
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(inputs
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`(;; Our ICU is too recent: “error: ‘UChar’ does not name a type“.
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;; ("icu4c" ,icu4c)
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("libjpeg" ,libjpeg)
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("libpng" ,libpng)
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("libtiff" ,libtiff)
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("libxml2" ,libxml2)
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("openssl" ,openssl)
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("zlib" ,zlib)))
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(native-inputs
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`(("doxygen" ,doxygen))) ; for HTML documentation
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(home-page "https://dcmtk.org")
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(synopsis "Libraries and programs implementing parts of the DICOM standard")
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(description "DCMTK is a collection of libraries and applications
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implementing large parts the DICOM standard. It includes software for
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examining, constructing and converting DICOM image files, handling offline
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media, sending and receiving images over a network connection, as well as
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demonstrative image storage and worklist servers.")
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(license (license:fsf-free
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"file://COPYRIGHT"
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"A union of the Apache 2.0 licence and various non-copyleft
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licences similar to the Modified BSD licence."))))
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(define-public mia
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(package
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(name "mia")
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(version "2.4.6")
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(source (origin
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(method url-fetch)
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(uri (string-append "mirror://sourceforge/mia/mia/"
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(version-major+minor version)
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"/mia-" version ".tar.xz"))
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(sha256
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(base32
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"0j4nd5z7i3v199jh7hqqhwd4g7snchizkc7rhzanpvngqg91m1pb"))))
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(build-system cmake-build-system)
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(arguments
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`(#:configure-flags
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(list "-DMIA_CREATE_NIPYPE_INTERFACES=0"
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"-DCMAKE_CXX_FLAGS=-fpermissive")))
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(inputs
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`(("boost" ,boost)
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("dcmtk" ,dcmtk)
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("doxygen" ,doxygen)
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("eigen" ,eigen)
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("fftw" ,fftw)
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("fftwf" ,fftwf)
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("gsl" ,gsl)
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("gts" ,gts)
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("hdf5" ,hdf5)
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("itpp" ,itpp)
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("libjpeg" ,libjpeg)
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("libpng" ,libpng)
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("libtiff" ,libtiff)
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("libxml" ,libxml2)
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("libxml++" ,libxml++)
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("maxflow" ,maxflow)
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("niftilib" ,niftilib)
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("nlopt" ,nlopt)
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("openexr" ,openexr)
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("python-lxml" ,python2-lxml)
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("vtk" ,vtk)))
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(native-inputs
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`(("pkg-config" ,pkg-config)
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("python" ,python-2)))
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(home-page "http://mia.sourceforge.net")
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(synopsis "Toolkit for gray scale medical image analysis")
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(description "MIA provides a combination of command line tools, plug-ins,
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and libraries that make it possible run image processing tasks interactively
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in a command shell and to prototype using the shell's scripting language. It
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is built around a plug-in structure that makes it easy to add functionality
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without compromising the original code base and it makes use of a wide variety
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of external libraries that provide additional functionality.")
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(license license:gpl3+)))
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(define-public vtk
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(package
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(name "vtk")
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(version "8.2.0")
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(source (origin
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(method url-fetch)
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(uri (string-append "https://vtk.org/files/release/"
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(version-major+minor version)
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"/VTK-" version ".tar.gz"))
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(sha256
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(base32
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"1fspgp8k0myr6p2a6wkc21ldcswb4bvmb484m12mxgk1a9vxrhrl"))))
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(build-system cmake-build-system)
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(arguments
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'(#:build-type "Release" ;Build without '-g' to save space.
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;; -DVTK_USE_SYSTEM_NETCDF:BOOL=TRUE requires netcdf_cxx
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#:configure-flags '("-DVTK_USE_SYSTEM_EXPAT:BOOL=TRUE"
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"-DVTK_USE_SYSTEM_FREETYPE:BOOL=TRUE"
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"-DVTK_USE_SYSTEM_HDF5:BOOL=TRUE"
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"-DVTK_USE_SYSTEM_JPEG:BOOL=TRUE"
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"-DVTK_USE_SYSTEM_JSONCPP:BOOL=TRUE"
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"-DVTK_USE_SYSTEM_LIBXML2:BOOL=TRUE"
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"-DVTK_USE_SYSTEM_OGGTHEORA:BOOL=TRUE"
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"-DVTK_USE_SYSTEM_PNG:BOOL=TRUE"
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"-DVTK_USE_SYSTEM_TIFF:BOOL=TRUE"
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"-DVTK_USE_SYSTEM_ZLIB:BOOL=TRUE")
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#:tests? #f)) ;XXX: no "test" target
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(inputs
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`(("libXt" ,libxt)
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("xorgproto" ,xorgproto)
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("libX11" ,libx11)
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("libxml2" ,libxml2)
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("mesa" ,mesa)
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("glu" ,glu)
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("expat" ,expat)
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("freetype" ,freetype)
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("hdf5" ,hdf5)
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("jpeg" ,libjpeg)
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("jsoncpp" ,jsoncpp)
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("libogg" ,libogg)
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("libtheora" ,libtheora)
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("png" ,libpng)
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("tiff" ,libtiff)
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("zlib" ,zlib)))
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(home-page "https://vtk.org/")
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(synopsis "Libraries for 3D computer graphics")
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(description
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"The Visualization Toolkit (VTK) is a C++ library for 3D computer graphics,
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image processing and visualization. It supports a wide variety of
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visualization algorithms including: scalar, vector, tensor, texture, and
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volumetric methods; and advanced modeling techniques such as: implicit
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modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay
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triangulation. VTK has an extensive information visualization framework, has
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a suite of 3D interaction widgets, supports parallel processing, and
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integrates with various databases on GUI toolkits such as Qt and Tk.")
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(license license:bsd-3)))
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;; itksnap needs an older variant of VTK.
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(define-public vtk-6
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(package (inherit vtk)
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(version "6.3.0")
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(source (origin
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(method url-fetch)
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(uri (string-append "https://vtk.org/files/release/"
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(version-major+minor version)
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"/VTK-" version ".tar.gz"))
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(sha256
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(base32
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"0pla1r5mvkgl4sl213gfdhzrypdgai0h3z5mfgm6p9jz9hsr794j"))))
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(inputs
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`(("jsoncpp" ,jsoncpp-for-tensorflow)
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,@(alist-delete "jsoncpp" (package-inputs vtk))))))
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(define-public opencv
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(package
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(name "opencv")
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(version "3.4.3")
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/opencv/opencv")
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(commit version)))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"06bc61r8myym4s8im10brdjfg4wxkrvsbhhl7vr1msdan2xddzi3"))
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(modules '((guix build utils)))
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(snippet
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'(begin
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;; Remove external libraries. We have all available in Guix:
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(delete-file-recursively "3rdparty")
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;; Milky icon set is non-free:
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(delete-file-recursively "modules/highgui/src/files_Qt/Milky")
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;; Some jars found:
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(for-each delete-file
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'("modules/java/test/pure_test/lib/junit-4.11.jar"
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"samples/java/sbt/sbt/sbt-launch.jar"))
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#t))))
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(build-system cmake-build-system)
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(arguments
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`(#:configure-flags
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(list "-DWITH_IPP=OFF"
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"-DWITH_ITT=OFF"
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"-DWITH_CAROTENE=OFF" ; only visible on arm/aarch64
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"-DENABLE_PRECOMPILED_HEADERS=OFF"
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;; CPU-Features:
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;; See cmake/OpenCVCompilerOptimizations.cmake
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;; (CPU_ALL_OPTIMIZATIONS) for a list of all optimizations
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;; BASELINE is the minimum optimization all CPUs must support
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;;
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;; DISPATCH is the list of optional dispatches.
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"-DCPU_BASELINE=SSE2"
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,@(match (%current-system)
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("x86_64-linux"
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'("-DCPU_DISPATCH=NEON;VFPV3;FP16;SSE;SSE2;SSE3;SSSE3;SSE4_1;SSE4_2;POPCNT;AVX;FP16;AVX2;FMA3;AVX_512F;AVX512_SKX"
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"-DCPU_DISPATCH_REQUIRE=SSE3,SSSE3,SSE4_1,SSE4_2,AVX,AVX2"))
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("armhf-linux"
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'("-DCPU_BASELINE_DISABLE=NEON")) ; causes build failures
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("aarch64-linux"
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'("-DCPU_BASELINE=NEON"
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"-DCPU_DISPATCH=NEON;VFPV3;FP16"))
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(_ '()))
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"-DBUILD_PERF_TESTS=OFF"
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"-DBUILD_TESTS=ON"
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(string-append "-DOPENCV_EXTRA_MODULES_PATH=" (getcwd)
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"/opencv-contrib/modules")
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;;Define test data:
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(string-append "-DOPENCV_TEST_DATA_PATH=" (getcwd)
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"/opencv-extra/testdata")
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;; Is ON by default and would try to rebuild 3rd-party protobuf,
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;; which we had removed, which would lead to an error:
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"-DBUILD_PROTOBUF=OFF"
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;; Rebuild protobuf files, because we have a slightly different
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;; version than the included one. If we would not update, we
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;; would get a compile error later:
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"-DPROTOBUF_UPDATE_FILES=ON"
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;; xfeatures2d disabled, because it downloads extra binaries from
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;; https://github.com/opencv/opencv_3rdparty
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;; defined in xfeatures2d/cmake/download_{vgg|bootdesc}.cmake
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;; Cmp this bug entry:
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;; https://github.com/opencv/opencv_contrib/issues/1131
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"-DBUILD_opencv_xfeatures2d=OFF")
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#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'disable-broken-tests
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(lambda _
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;; These tests fails with:
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;; vtkXOpenGLRenderWindow (0x723990): Could not find a decent config
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;; I think we have no OpenGL support with the Xvfb.
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(substitute* '("modules/viz/test/test_tutorial3.cpp"
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"modules/viz/test/test_main.cpp"
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"modules/viz/test/tests_simple.cpp"
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"modules/viz/test/test_viz3d.cpp")
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(("(TEST\\(Viz, )([a-z].*\\).*)" all pre post)
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(string-append pre "DISABLED_" post)))
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;; This one fails with "unknown file: Failure"
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;; But I couldn't figure out which file was missing:
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(substitute* "../opencv-contrib/modules/face/test/test_face_align.cpp"
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(("(TEST\\(CV_Face_FacemarkKazemi, )(can_detect_landmarks\\).*)"
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all pre post)
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(string-append pre "DISABLED_" post)))
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;; Failure reason: Bad accuracy
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;; Incorrect count of accurate poses [2nd case]: 90.000000 / 94.000000
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(substitute* "../opencv-contrib/modules/rgbd/test/test_odometry.cpp"
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(("(TEST\\(RGBD_Odometry_Rgbd, )(algorithmic\\).*)" all pre post)
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(string-append pre "DISABLED_" post)))
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#t))
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(add-after 'unpack 'unpack-submodule-sources
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(lambda* (#:key inputs #:allow-other-keys)
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(mkdir "../opencv-extra")
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(mkdir "../opencv-contrib")
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(copy-recursively (assoc-ref inputs "opencv-extra")
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"../opencv-extra")
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(invoke "tar" "xvf"
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(assoc-ref inputs "opencv-contrib")
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"--strip-components=1"
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"-C" "../opencv-contrib")))
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(add-after 'set-paths 'add-ilmbase-include-path
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(lambda* (#:key inputs #:allow-other-keys)
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||
;; OpenEXR propagates ilmbase, but its include files do not appear
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||
;; in the CPATH, so we need to add "$ilmbase/include/OpenEXR/" to
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||
;; the CPATH to satisfy the dependency on "ImathVec.h".
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(setenv "CPATH"
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(string-append (assoc-ref inputs "ilmbase")
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||
"/include/OpenEXR"
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":" (or (getenv "CPATH") "")))
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#t))
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||
(add-before 'check 'start-xserver
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(lambda* (#:key inputs #:allow-other-keys)
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(let ((xorg-server (assoc-ref inputs "xorg-server"))
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||
(disp ":1"))
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||
(setenv "HOME" (getcwd))
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||
(setenv "DISPLAY" disp)
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||
;; There must be a running X server and make check doesn't start one.
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;; Therefore we must do it.
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(zero? (system (format #f "~a/bin/Xvfb ~a &" xorg-server disp)))))))))
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(native-inputs
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||
`(("pkg-config" ,pkg-config)
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||
("xorg-server" ,xorg-server) ; For running the tests
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||
("opencv-extra"
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,(origin
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||
(method git-fetch)
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||
(uri (git-reference
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||
(url "https://github.com/opencv/opencv_extra")
|
||
(commit version)))
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||
(file-name (git-file-name "opencv_extra" version))
|
||
(sha256
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||
(base32 "08p5xnq8n1jw8svvz0fnirfg7q8dm3p4a5dl7527s5xj0f9qn7lp"))))
|
||
("opencv-contrib"
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||
,(origin
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||
(method git-fetch)
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||
(uri (git-reference
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||
(url "https://github.com/opencv/opencv_contrib")
|
||
(commit version)))
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||
(file-name (git-file-name "opencv_contrib" version))
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||
(patches (search-patches "opencv-rgbd-aarch64-test-fix.patch"))
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||
(sha256
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(base32 "1f334glf39nk42mpqq6j732h3ql2mpz89jd4mcl678s8n73nfjh2"))))))
|
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(inputs `(("libjpeg" ,libjpeg)
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("libpng" ,libpng)
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("jasper" ,jasper)
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;; ffmpeg 4.0 causes core dumps in tests.
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("ffmpeg" ,ffmpeg-3.4)
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("libtiff" ,libtiff)
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("hdf5" ,hdf5)
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("libgphoto2" ,libgphoto2)
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("libwebp" ,libwebp)
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("zlib" ,zlib)
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||
("gtkglext" ,gtkglext)
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("openexr" ,openexr)
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||
("ilmbase" ,ilmbase)
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("gtk+" ,gtk+-2)
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("python-numpy" ,python-numpy)
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("protobuf" ,protobuf)
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("vtk" ,vtk)
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("python" ,python)))
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;; These three CVEs are not a problem of OpenCV, see:
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;; https://github.com/opencv/opencv/issues/10998
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(properties '((lint-hidden-cve . ("CVE-2018-7712"
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"CVE-2018-7713"
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"CVE-2018-7714"))))
|
||
(synopsis "Computer vision library")
|
||
(description "OpenCV is a library aimed at
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real-time computer vision, including several hundred computer
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vision algorithms. It can be used to do things like:
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|
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@itemize
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||
@item image and video input and output
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||
@item image and video processing
|
||
@item displaying
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||
@item feature recognition
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@item segmentation
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@item facial recognition
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@item stereo vision
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@item structure from motion
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@item augmented reality
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||
@item machine learning
|
||
@end itemize\n")
|
||
(home-page "https://opencv.org/")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public vips
|
||
(package
|
||
(name "vips")
|
||
(version "8.7.4")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append
|
||
"https://github.com/libvips/libvips/releases/download/v"
|
||
version "/vips-" version ".tar.gz"))
|
||
(sha256
|
||
(base32 "01gjhcrl6zj7mcj1al717v5jsniahplqhz1xkfh2j78vyfl1hxff"))))
|
||
(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 "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 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) ; 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+)))
|
||
|
||
(define-public vxl
|
||
(package
|
||
(name "vxl")
|
||
(version "2.0.2")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/vxl/vxl.git")
|
||
(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
|
||
`(("libgeotiff" ,libgeotiff)
|
||
("libtiff" ,libtiff)
|
||
("libjpeg" ,libjpeg)
|
||
("libpng" ,libpng)
|
||
("zlib" ,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.git")
|
||
(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)
|
||
("libpng" ,libpng)
|
||
("libtiff" ,libtiff)
|
||
("mesa" ,mesa-opencl)
|
||
("perl" ,perl)
|
||
("python" ,python)
|
||
("tbb" ,tbb)
|
||
("vxl" ,vxl-1)
|
||
("zlib" ,zlib)))
|
||
(native-inputs
|
||
`(("googletest" ,googletest)
|
||
("pkg-config" ,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"))))
|
||
(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\\}\\)")
|
||
""))
|
||
#t))
|
||
(add-after 'unpack 'disable-gui-tests
|
||
(lambda _
|
||
;; The GUI tests just time out.
|
||
(substitute* "CMakeLists.txt"
|
||
((" (Workspace|DiffSpace|ProbeIntensity|RegionCompetition\
|
||
|RandomForest|RandomForestBailOut)")
|
||
""))
|
||
#t))
|
||
(add-after 'unpack 'make-reproducible
|
||
(lambda _
|
||
(substitute* "CMakeLists.txt"
|
||
(("TODAY\\(SNAP_VERSION_COMPILE_DATE\\)")
|
||
"SET(SNAP_VERSION_COMPILE_DATE \"(removed for reproducibility)\")"))
|
||
#t))
|
||
(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")
|
||
#t))
|
||
(add-after 'unpack 'fix-includes
|
||
(lambda _
|
||
(substitute* "GUI/Model/RegistrationModel.cxx"
|
||
(("<vnl_symmetric_eigensystem.h>")
|
||
"<vnl/algo/vnl_symmetric_eigensystem.h>"))
|
||
#t))
|
||
(add-before 'check 'prepare-tests
|
||
(lambda _
|
||
;; Needed by at least one test.
|
||
(setenv "HOME" "/tmp")
|
||
#t))
|
||
(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"))))
|
||
#t))))))
|
||
(inputs
|
||
`(("curl" ,curl)
|
||
("fftw" ,fftw)
|
||
("fftwf" ,fftwf)
|
||
("glu" ,glu)
|
||
("hdf5" ,hdf5)
|
||
("mesa" ,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.
|
||
("itk" ,insight-toolkit-4.12)
|
||
("vtk" ,vtk-6)
|
||
("qtbase" ,qtbase)
|
||
("qtdeclarative" ,qtdeclarative)
|
||
("qttools" ,qttools)
|
||
("vxl" ,vxl-1)
|
||
("zlib" ,zlib)))
|
||
(native-inputs
|
||
`(("googletest" ,googletest)
|
||
("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.git")
|
||
(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.git")
|
||
(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+)))
|