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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>
;;;
;;; 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 fontutils)
#:use-module (gnu packages gl)
#: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 serialization)
#:use-module (gnu packages xiph)
#:use-module (gnu packages xml)
#:use-module (gnu packages xorg))
;; 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 "7.1.0")
(source (origin
(method url-fetch)
(uri (string-append "http://www.vtk.org/files/release/"
(version-major+minor version)
"/VTK-" version ".tar.gz"))
(sha256
(base32
"0yj96z58haan77gzilnqp7xpf8hg5jk11a3jx55p2ksd400s0gjz"))))
(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)
("xproto" ,xproto)
("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 "http://www.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)))
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