Merge branch 'master' into core-updates

1 files changed, 130 insertions, 0 deletions

diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-processing.scm
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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+)))