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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>
+;;;
+;;; 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 build-system cmake)
+ #:use-module (guix build-system gnu)
+ #:use-module (gnu packages)
+ #:use-module (gnu packages algebra)
+ #:use-module (gnu packages boost)
+ #:use-module (gnu packages compression)
+ #:use-module (gnu packages documentation)
+ #:use-module (gnu packages gnome)
+ #:use-module (gnu packages graphics)
+ #:use-module (gnu packages graphviz)
+ #:use-module (gnu packages image)
+ #:use-module (gnu packages maths)
+ #:use-module (gnu packages perl)
+ #:use-module (gnu packages pkg-config)
+ #:use-module (gnu packages python)
+ #:use-module (gnu packages xml)
+ #:use-module (gnu packages vtk))
+
+;; 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 "2.4.4")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "mirror://sourceforge/mia/mia/"
+ (version-major+minor version)
+ "/mia-" version ".tar.xz"))
+ (sha256
+ (base32
+ "124gvf8nkls59mlnx8ynq00n9zrah7a54gsywafx7qmfr0y95ra7"))))
+ (build-system cmake-build-system)
+ (arguments
+ `(#:configure-flags
+ (list "-DMIA_CREATE_NIPYPE_INTERFACES=0"
+ (string-append "-DCMAKE_INSTALL_LIBDIR="
+ (assoc-ref %outputs "out") "/lib")
+ "-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+)))