Subject: [PATCH 6/7] gnu: Add mia.
From: John Darrington <[email-masked]>
To: [email-masked]
Cc: John Darrington <[email-masked]>
Date: Wed, 15 Mar 2017 21:05:23 +0100
List-Id: <debbugs-submit.debbugs.gnu.org>

* gnu/packages/image-processing.scm (mia): New variable.
---
 gnu/packages/image-processing.scm | 75 ++++++++++++++++++++++++++++++++++++++-
 1 file changed, 74 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-processing.scm
index e1ad93e..e080569 100644
--- a/gnu/packages/image-processing.scm
+++ b/gnu/packages/image-processing.scm
@@ -21,12 +21,25 @@
   #:use-module (guix packages)
   #:use-module (guix utils)
   #:use-module (guix download)
+  #:use-module (guix git-download)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system cmake)
   #: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 maths)
+  #:use-module (gnu packages xml)
   #:use-module (gnu packages image)
-  #:use-module (gnu packages perl))
+  #:use-module (gnu packages perl)
+  #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages python)
+  #:use-module (gnu packages tbb)
+  #:use-module (gnu packages vtk))
 
 (define-public dcmtk
   (package
@@ -73,3 +86,63 @@ demonstrative image storage and worklist servers.")
               "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 "2.4.3")
+    (source (origin
+              ;; There are too many issues with the released version which
+              ;; prevent a clean build and test under Guix.  So until the next
+              ;; release I suggest we use this git checkout.
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://git.code.sf.net/p/mia/mia2")
+                    (commit "d91cade30a10f179bba8c8e48b84983a296d2c33")))
+              (sha256
+               (base32
+                "0y8ihqbliqy21fph3dm5h6k2nvjbajx4y0mn351x990r9y0767vz"))
+              (file-name (string-append name "-" version))))
+    (build-system cmake-build-system)
+    (arguments `(#:configure-flags `("-DMIA_CREATE_NIPYPE_INTERFACES=0"
+                                     ,(string-append "-DCMAKE_INSTALL_LIBDIR="
+                                                     (assoc-ref %outputs "out")
+                                                     "/lib")
+                                     ;; According to upstream this is necessary
+                                     ;; with g++-4.9.x because the std::regex
+                                     ;; library doesn't work reliably.
+                                     "-DMIA_USE_BOOST_REGEX=ON"
+                                     "-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" ,[email-masked])))
+    (native-inputs `(("pkg-config"   ,pkg-config)
+                     ("python" ,python-2)))
+    (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.")
+    (home-page "http://mia.sourceforge.net")
+    (license license:gpl3+)))
-- 
2.1.4