gnu: Add elastix.

* gnu/packages/image-processing.scm (elastix): New variable.
* gnu/packages/patches/elastix-1404.patch: New file.
* gnu/local.mk (dist_patch_DATA): Record it.

Change-Id: Ic3b76c70afe2fc7ddb0f2516204f76e5690143a9

3 files changed, 84 insertions, 1 deletions

diff --git a/gnu/local.mk b/gnu/local.mk
index e8e144294e2..a348b2916f1 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1220,6 +1220,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/dwarves-threading-reproducibility.patch  \
   %D%/packages/patches/efitools-riscv64-support.patch           \
   %D%/packages/patches/efivar-fix-fprint-format.patch           \
+  %D%/packages/patches/elastix-1404.patch                       \
   %D%/packages/patches/eigen-fix-strict-aliasing-bug.patch      \
   %D%/packages/patches/einstein-build.patch                     \
   %D%/packages/patches/elfutils-tests-ptrace.patch              \
diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-processing.scm
index 01d829e72ac..06452038dba 100644
--- a/gnu/packages/image-processing.scm
+++ b/gnu/packages/image-processing.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2017 John Darrington <jmd@gnu.org>
-;;; Copyright © 2017, 2019, 2022, 2024 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2017, 2019, 2021-2026 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2014, 2021-2023, 2026 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2014 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.org>
@@ -1771,6 +1771,56 @@ full-featured UI aimed at clinical researchers.")
     ;; This includes the submodules greedy, c3d and digestible.
     (license license:gpl3+))))
 
+(define-public elastix
+  (package
+    (name "elastix")
+    (version "5.3.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/SuperElastix/elastix")
+              (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0sgw4cz4x6f78n6iqn87ll6wad32y67lmzvqfdfw1pzjkxbwzwyr"))
+       (patches
+        (search-patches "elastix-1404.patch"))))
+    (properties '((tunable? . #t)))
+    (build-system cmake-build-system)
+    (arguments
+     (list
+      #:configure-flags
+      #~(list "-DELASTIX_USE_EIGEN=ON"
+              "-DELASTIX_ENABLE_PACKAGER:BOOL=OFF"
+              "-DELASTIX_BUILD_EXECUTABLE:BOOL=ON"
+              "-DCMAKE_CXX_FLAGS=-fPIC"
+              "-DCMAKE_CXX_STANDARD=17"
+              "-DBUILD_TESTING:BOOL=ON")
+      ;; These tests fail and are skipped in upstream CI.
+      #:test-exclude (string-join
+                      (list "elastix_run_example_COMPARE_IM"
+                            (string-append "elastix_run_3DCT_lung.MI.bspline."
+                                           "ASGD.001_COMPARE_TP"))
+                      "|")))
+    (inputs (list charls
+                  dcmtk
+                  eigen
+                  fftw
+                  insight-toolkit
+                  libpng
+                  libtiff
+                  zlib))
+    (home-page "https://elastix.dev/")
+    (synopsis "Image registration toolbox")
+    (description
+     "Elastix is a toolbox for rigid and nonrigid registration of images.  The
+software consists of a collection of algorithms that are commonly used to
+perform (medical) image registration: the task of finding a spatial
+transformation, mapping one image (the fixed image) to another (the moving
+image), by optimizing relevant image similarity metrics.")
+    (license license:asl2.0)))
+
 (define-public metapixel
   ;; Follow stable branch.
   (let ((commit "98ee9daa093b6c334941242e63f90b1c2876eb4f"))
diff --git a/gnu/packages/patches/elastix-1404.patch b/gnu/packages/patches/elastix-1404.patch
new file mode 100644
index 00000000000..c98940c05fc
--- /dev/null
+++ b/gnu/packages/patches/elastix-1404.patch
@@ -0,0 +1,32 @@
+From b54984063cd61636c57add80522bad23f70bb00a Mon Sep 17 00:00:00 2001
+From: Niels Dekker <N.Dekker@lumc.nl>
+Date: Tue, 3 Feb 2026 14:03:06 +0100
+Subject: [PATCH] ENH: Add relative path to lib directory to RPATH on Linux and
+ MacOS
+
+Addresses issue #1402, Avoid "error while loading shared libraries" on Linux
+---
+ Core/CMakeLists.txt | 10 ++++++++--
+ 1 file changed, 8 insertions(+), 2 deletions(-)
+
+diff --git a/Core/CMakeLists.txt b/Core/CMakeLists.txt
+index 3b70abf12..204782b29 100644
+--- a/Core/CMakeLists.txt
++++ b/Core/CMakeLists.txt
+@@ -277,8 +277,14 @@ set(ELASTIX_LIBRARIES elastix_lib transformix_lib PARENT_SCOPE)
+ 
+ if(ELASTIX_BUILD_EXECUTABLE AND NOT WIN32)
+   # Tell the executables where to find the required .so files.
+-  set_target_properties(elastix_exe transformix_exe
+-    PROPERTIES INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib:${ITK_DIR}")
++  # Supports having the executables in bin, and the .so files in the lib directory next to the bin.
++  if (APPLE)
++    set_target_properties(elastix_exe transformix_exe
++      PROPERTIES BUILD_RPATH "@executable_path/../lib" INSTALL_RPATH "@executable_path/../lib:${CMAKE_INSTALL_PREFIX}/lib:${ITK_DIR}")
++  else()
++    set_target_properties(elastix_exe transformix_exe
++      PROPERTIES BUILD_RPATH "\$ORIGIN/../lib" INSTALL_RPATH "\$ORIGIN/../lib:${CMAKE_INSTALL_PREFIX}/lib:${ITK_DIR}")
++  endif()
+ endif()
+ 
+ if(ELASTIX_BUILD_EXECUTABLE AND NOT ELASTIX_NO_INSTALL_EXECUTABLES)