gnu: insight-toolkit: Update to 5.4.4.

* gnu/packages/image-processing (insight-toolkit): Update to 5.4.4.
[source] Switch to git-fetch; apply patch.
[arguments]<#:configure-flags>: Add -DITK_USE_SYSTEM_SWIG=ON,
-DCMAKE_BUILD_WITH_INSTALL_RPATH=ON, -DITK_USE_PYTHON_LIMITED_API=OFF and
-DBUILD_TESTING=OFF.  Add -DHDF5_DIR set to HDF5's lib/cmake.
[inputs]: Add libaec.
[native-inputs]: Add git-minimal; replace swig with swig-next.
* gnu/packages/patches/insight-toolkit-fix-build.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register patch.

Change-Id: Ifbf73709e773649fb00c2d46848d3418daaf98c1
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu/local.mk

@@ -1623,6 +1623,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/instead-use-games-path.patch		\
   %D%/packages/patches/intltool-perl-compatibility.patch	\
   %D%/packages/patches/inetutils-hurd64.patch			\
+  %D%/packages/patches/insight-toolkit-fix-build.patch			\
   %D%/packages/patches/irrlicht-use-system-libs.patch		\
   %D%/packages/patches/irrlicht-link-against-needed-libs.patch	\
   %D%/packages/patches/isl-0.11.1-aarch64-support.patch	\

gnu/packages/image-processing.scm

@@ -24,6 +24,7 @@
 ;;; Copyright © 2022 Paul A. Patience <paul@apatience.com>
 ;;; Copyright © 2023 Cairn <cairn@pm.me>
 ;;; Copyright © 2024 Nicolas Graves <ngraves@ngraves.fr>
+;;; Copyright © 2025 Jake Forster <jakecameron.forster@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1238,15 +1239,20 @@ libraries designed for computer vision research and implementation.")
 (define-public insight-toolkit
   (package
     (name "insight-toolkit")
-    (version "5.0.0")
+    (version "5.4.4")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/InsightSoftwareConsortium/ITK/"
-                           "releases/download/v" version "/InsightToolkit-"
-                           version ".tar.xz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/InsightSoftwareConsortium/ITK")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "0bs63mk4q8jmx38f031jy5w5n9yy5ng9x8ijwinvjyvas8cichqi"))))
+        (base32 "1l5rby8jj8726k380aivycmhn56cz56mr9k3r56c8hkkrfwwng50"))
+       ;; This patch is required to build with both ITK_USE_GPU=ON and
+       ;; ITK_WRAP_PYTHON=ON.
+       ;; <https://github.com/InsightSoftwareConsortium/ITK/pull/4842>
+       (patches (search-patches "insight-toolkit-fix-build.patch"))))
     (build-system cmake-build-system)
     (outputs '("out" "python"))
     (arguments
@@ -1255,7 +1261,15 @@ libraries designed for computer vision research and implementation.")
            #~(list "-DITK_USE_GPU=ON"
                    "-DITK_USE_SYSTEM_LIBRARIES=ON"
                    "-DITK_USE_SYSTEM_CASTXML=ON"
+                   "-DITK_USE_SYSTEM_SWIG=ON"
+                   (string-append "-DHDF5_DIR=" #$(this-package-input "hdf5")
+                                  "/lib/cmake")
                    "-DBUILD_SHARED_LIBS=ON"
+                   ;; Without this flag, there are shared libraries installed
+                   ;; in PY_SITE_PACKAGES_PATH/itk instead of #$output/lib and
+                   ;; RUNPATHs contain the *build directory* of
+                   ;; PY_SITE_PACKAGES_PATH/itk.
+                   "-DCMAKE_BUILD_WITH_INSTALL_RPATH=ON"
                    "-DITK_WRAPPING=ON"
                    "-DITK_WRAP_PYTHON=ON"
                    "-DITK_DYNAMIC_LOADING=ON"
@@ -1267,7 +1281,10 @@ libraries designed for computer vision research and implementation.")
                                           "/lib/python" python-version
                                           "/site-packages")))
                      (string-append "-DPY_SITE_PACKAGES_PATH=" python-lib-path))
-                   "-DCMAKE_CXX_STANDARD=17")
+                   ;; Python is not built with Py_LIMITED_API.
+                   "-DITK_USE_PYTHON_LIMITED_API=OFF"
+                   "-DCMAKE_CXX_STANDARD=17"
+                   "-DBUILD_TESTING=OFF")
 
            #:phases #~(modify-phases %standard-phases
                         (add-after 'unpack 'do-not-tune
@@ -1298,6 +1315,7 @@ libraries designed for computer vision research and implementation.")
            fftw
            fftwf
            hdf5
+           libaec
            libjpeg-turbo
            libpng
            libtiff
@@ -1308,7 +1326,7 @@ libraries designed for computer vision research and implementation.")
            vxl-1
            zlib))
     (native-inputs
-     (list castxml pkg-config swig which))
+     (list castxml git-minimal pkg-config swig-next which))
 
     ;; The 'CMake/ITKSetStandardCompilerFlags.cmake' file normally sets
     ;; '-mtune=native -march=corei7', suggesting there's something to be

gnu/packages/patches/insight-toolkit-fix-build.patch

@@ -0,0 +1,43 @@
+From 3e90110ece80124d38641b3a1d02a9127f56eb25 Mon Sep 17 00:00:00 2001
+From: David Allemang <david.allemang@kitware.com>
+Date: Mon, 9 Sep 2024 13:19:43 -0400
+Subject: [PATCH] COMP: Fix Python GPU Wrapping
+
+---
+ .../GPUImageFilterBase/wrapping/itkGPUCastImageFilter.wrap    | 4 ++--
+ .../wrapping/itkGPUDiscreteGaussianImageFilter.wrap           | 3 +++
+ 2 files changed, 5 insertions(+), 2 deletions(-)
+
+diff --git a/Modules/Filtering/GPUImageFilterBase/wrapping/itkGPUCastImageFilter.wrap b/Modules/Filtering/GPUImageFilterBase/wrapping/itkGPUCastImageFilter.wrap
+index 7c1116884d7..c70af7d8446 100644
+--- a/Modules/Filtering/GPUImageFilterBase/wrapping/itkGPUCastImageFilter.wrap
++++ b/Modules/Filtering/GPUImageFilterBase/wrapping/itkGPUCastImageFilter.wrap
+@@ -23,7 +23,7 @@ foreach(from ${from_types})
+ endforeach()
+ itk_end_wrap_class()
+
+-itk_wrap_class("itk::CastImageFilter" POINTER)
++itk_wrap_class("itk::CastImageFilter" POINTER_WITH_SUPERCLASS)
+ foreach(d ${ITK_WRAP_IMAGE_DIMS})
+   # Add from == to pixel type first for preference
+   foreach(to ${to_types})
+@@ -183,7 +183,7 @@ foreach(d ${ITK_WRAP_IMAGE_DIMS})
+ endforeach()
+ itk_end_wrap_class()
+
+-itk_wrap_class("itk::GPUCastImageFilter" POINTER)
++itk_wrap_class("itk::GPUCastImageFilter" POINTER_WITH_SUPERCLASS)
+ foreach(d ${ITK_WRAP_IMAGE_DIMS})
+   # Add from == to pixel type first for preference
+   foreach(to ${to_types})
+diff --git a/Modules/Filtering/GPUSmoothing/wrapping/itkGPUDiscreteGaussianImageFilter.wrap b/Modules/Filtering/GPUSmoothing/wrapping/itkGPUDiscreteGaussianImageFilter.wrap
+index 2477c7876f0..0cfe9c2bd4a 100644
+--- a/Modules/Filtering/GPUSmoothing/wrapping/itkGPUDiscreteGaussianImageFilter.wrap
++++ b/Modules/Filtering/GPUSmoothing/wrapping/itkGPUDiscreteGaussianImageFilter.wrap
+@@ -1,3 +1,6 @@
++set(types "${WRAP_ITK_SCALAR}")
++itk_wrap_include("itkGPUImage.h")
++
+ itk_wrap_class("itk::DiscreteGaussianImageFilter" POINTER)
+ foreach(d ${ITK_WRAP_IMAGE_DIMS})
+   foreach(t ${types})