M gnu/local.mk => gnu/local.mk +0 -1
@@ 1634,7 1634,6 @@ dist_patch_DATA = \
%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 \
- %D%/packages/patches/itk-snap-alt-glibc-compat.patch \
%D%/packages/patches/jamesdsp-fix-bulid-on-pipewire-1.4.0.patch\
%D%/packages/patches/jami-disable-webengine.patch \
%D%/packages/patches/jami-enable-testing.patch \
M gnu/packages/image-processing.scm => gnu/packages/image-processing.scm +105 -110
@@ 106,6 106,7 @@
#:use-module (gnu packages serialization)
#:use-module (gnu packages sphinx)
#:use-module (gnu packages sqlite)
+ #:use-module (gnu packages ssh)
#:use-module (gnu packages swig)
#:use-module (gnu packages tbb)
#:use-module (gnu packages textutils)
@@ 1477,137 1478,131 @@ combine the information contained in both.")
#~(cons* "-DCMAKE_CXX_FLAGS=-std=c++14" #$cf))))))
(define-public itk-snap
+ ;; The latest release, 4.2.2, segmentation faults on startup.
+ ;; The commit is version 4.4.0-alpha3.
+ (let ((commit "65251254d44d68a6c0530984169784e35de020dd")
+ (revision "0"))
(package
(name "itk-snap")
- (version "3.8.0")
+ (version (git-version "4.2.2" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
- (url "https://git.code.sf.net/p/itk-snap/src")
- (commit (string-append "v" version))))
+ (url "https://github.com/pyushkevich/itksnap")
+ (commit commit)))
(file-name (git-file-name name version))
(sha256
- (base32 "15i5ixpryfrbf3vrrb5rici8fb585f25k0v1ljds16bp1f1msr4q"))
- (patches (search-patches "itk-snap-alt-glibc-compat.patch"))))
+ (base32 "07dgcfklc55yj3ldcq6fc5fil8qfrv7z6c3xhbd293kz7kpjr4yc"))))
(build-system cmake-build-system)
(arguments
- `(#:configure-flags
- (list "-DSNAP_VERSION_GIT_SHA1=release"
- "-DSNAP_VERSION_GIT_BRANCH=release"
- "-DSNAP_VERSION_GIT_TIMESTAMP=0"
- "-DSNAP_PACKAGE_QT_PLUGINS=OFF"
- "-DCMAKE_POSITION_INDEPENDENT_CODE=ON"
- ;; ISO C++17 does not allow dynamic exception specifications.
- "-DCMAKE_CXX_STANDARD=14")
- #:phases
- (modify-phases %standard-phases
- ;; During the installation phase all libraries provided by all
- ;; dependencies will be copied to the lib directory. That's insane,
- ;; so we disable this.
- (add-after 'unpack 'do-not-copy-dependencies
- (lambda _
- (substitute* "CMakeLists.txt"
- (("install_qt5_executable\
+ (list
+ #:configure-flags
+ #~(list "-DSNAP_VERSION_GIT_BRANCH=release"
+ "-DSNAP_PACKAGE_QT_PLUGINS=OFF")
+ #:phases
+ #~(modify-phases %standard-phases
+ ;; During the installation phase all libraries provided by all
+ ;; dependencies will be copied to the lib directory. That's insane,
+ ;; so we disable this.
+ (add-after 'unpack 'do-not-copy-dependencies
+ (lambda _
+ (substitute* "CMakeLists.txt"
+ (("install_qt5_executable\
\\(\\$\\{SNAP_MAIN_INSTALL_DIR\\}/\\$\\{SNAP_EXE\\}\\)")
- ""))))
- (add-after 'unpack 'disable-gui-tests
- (lambda _
- ;; The GUI tests just time out.
- (substitute* "CMakeLists.txt"
- ((" (Workspace|DiffSpace|ProbeIntensity|RegionCompetition\
-|RandomForest|RandomForestBailOut)")
- ""))))
- (add-after 'unpack 'make-reproducible
- (lambda _
- (substitute* "CMakeLists.txt"
- (("TODAY\\(SNAP_VERSION_COMPILE_DATE\\)")
- "SET(SNAP_VERSION_COMPILE_DATE \"(removed for reproducibility)\")"))))
- (add-after 'unpack 'prepare-submodules
- (lambda* (#:key inputs #:allow-other-keys)
- (rmdir "Submodules/c3d")
- (copy-recursively (assoc-ref inputs "c3d-src")
- "Submodules/c3d")
- (substitute* '("Submodules/c3d/adapters/BiasFieldCorrectionN4.cxx"
- "Submodules/c3d/adapters/ApplyMetric.cxx")
- (("vcl_") "std::"))
- (rmdir "Submodules/greedy")
- (symlink (assoc-ref inputs "greedy-src")
- "Submodules/greedy")))
- (add-after 'unpack 'fix-includes
- (lambda _
- (substitute* "GUI/Model/RegistrationModel.cxx"
- (("<vnl_symmetric_eigensystem.h>")
- "<vnl/algo/vnl_symmetric_eigensystem.h>"))))
- (add-before 'check 'prepare-tests
- (lambda _
- ;; Needed by at least one test.
- (setenv "HOME" "/tmp")))
- (add-after 'install 'wrap-executable
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out")))
- (wrap-program (string-append out "/bin/itksnap")
- `("QT_PLUGIN_PATH" ":" prefix
- ,(map (lambda (label)
- (string-append (assoc-ref inputs label)
- "/lib/qt5/plugins"))
- '("qtbase" "qtdeclarative"))))))))))
+ ""))))
+ (add-after 'unpack 'disable-gui-tests
+ (lambda _
+ ;; The GUI tests just segmentation fault.
+ (substitute* "CMakeLists.txt"
+ ((" (Workspace|DiffSpace|ProbeIntensity|RegionCompetition\
+|RandomForest|RandomForestBailOut|NaNs|4DContinuousRenderingD|EdgeAttraction\
+|EchoCartesianDicomLoading|LabelSmoothing|PreferencesDialog|MeshImport\
+|MeshWorkspace|SegmentationMesh|VolumeRendering|Reloading|4DToMC|MCTo4D\
+|DeformationGrid)")
+ ""))))
+ (add-after 'unpack 'make-reproducible
+ (lambda _
+ (substitute* "CMakeLists.txt"
+ (("TODAY\\(SNAP_VERSION_COMPILE_DATE\\)")
+ "SET(SNAP_VERSION_COMPILE_DATE \"(removed for reproducibility)\")"))))
+ (add-after 'unpack 'prepare-submodules
+ (lambda _
+ (rmdir "Submodules/c3d")
+ (symlink #$(this-package-native-input "c3d-checkout")
+ "Submodules/c3d")
+ (rmdir "Submodules/digestible")
+ (symlink #$(this-package-native-input "digestible-checkout")
+ "Submodules/digestible")
+ (rmdir "Submodules/greedy")
+ (symlink #$(this-package-native-input "greedy-checkout")
+ "Submodules/greedy")))
+ (add-after 'unpack 'remove-bundled-jsoncpp
+ (lambda _
+ (substitute* "CMakeLists.txt"
+ ((" Common/JSon/jsoncpp\\.cpp") ""))))
+ (add-before 'check 'prepare-tests
+ (lambda _
+ ;; Needed by at least one test.
+ (setenv "HOME" "/tmp")))
+ (add-after 'install 'wrap-executable
+ (lambda _
+ (wrap-program (string-append #$output "/bin/itksnap")
+ (list
+ "QT_PLUGIN_PATH"
+ 'suffix
+ (list (string-append #$(this-package-input "qtbase")
+ "/lib/qt6/plugins")
+ (string-append #$(this-package-input "qtdeclarative")
+ "/lib/qt6/plugins")))))))))
(inputs
- (list bash-minimal
- curl
- fftw
- fftwf
+ (list curl
+ freetype
+ glew
glu
- hdf5
+ insight-toolkit-legacy
+ jsoncpp
+ libssh
mesa-opencl
- ;; This package does not build with either insight-toolkit 5.0.0
- ;; and not with 4.13. It really needs to be 4.12.
- insight-toolkit-4.12
- vtk-7
- qtbase-5
- qtdeclarative-5
- vxl-1
- zlib))
+ qtbase
+ qtdeclarative
+ vtk))
(native-inputs
- `(("googletest" ,googletest)
- ("qttools-5" ,qttools-5)
- ("pkg-config" ,pkg-config)
- ("c3d-src"
- ,(let* ((commit "f521358db26e00002c911cc47bf463b043942ad3")
- (revision "1")
- (version (git-version "0" revision commit)))
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/pyushkevich/c3d")
- (commit commit)))
- (file-name (git-file-name "c3d" version))
- (sha256
- (base32
- "0kyv3rxrxwr8c3sa9zv01lsnhk95b27gx1s870k3yi8qp52h7bx3")))))
- ;; We are using an arbitrary commit from 2017 because the latest
- ;; version breaks the build...
- ("greedy-src"
- ,(let* ((commit "97e340f7e8e66597599144947775e6039e79a0d3")
- (revision "1")
- (version (git-version "0" revision commit)))
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/pyushkevich/greedy")
- (commit commit)))
- (file-name (git-file-name "greedy" version))
- (sha256
- (base32
- "0k5bc9za4jrc8z9dj08z1rkcp5xf0gnd1d2jmi1w9ny4vxh2q2ab")))))))
+ (list
+ doxygen
+ ;; Use the submodule commits in this version of ITK-SNAP.
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/pyushkevich/c3d")
+ (commit "a86a2a32db8635c1535522332fee68bc56eacaa2")))
+ (file-name "c3d-checkout")
+ (sha256
+ (base32 "0da3ikx7pqlrmvhkmzil269j6kyd84pphy1mls8v69gmzl89piis")))
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/pyushkevich/digestible")
+ (commit "1b66709e99c43d280bb472e1a0e36185ef2ea412")))
+ (file-name "digestible-checkout")
+ (sha256
+ (base32 "1m1b954prq6l3byfdgxw2y17xsg81agd516g5n6ps60dqnxw8hqs")))
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/pyushkevich/greedy")
+ (commit "f10152c5374da08ee024c4c60ef8882876bd0808")))
+ (file-name "greedy-checkout")
+ (sha256
+ (base32 "0xk1l0h4wis4nkfwjnvh624bdlhy7l26djibk4l00wzv0vvq21qv")))))
(home-page "https://sourceforge.net/p/itk-snap/")
(synopsis "Medical image segmentation")
(description "ITK-SNAP is a tool for segmenting anatomical structures in
medical images. It provides an automatic active contour segmentation
pipeline, along with supporting a manual segmentation toolbox. ITK-SNAP has a
full-featured UI aimed at clinical researchers.")
- ;; This includes the submodules greedy and c3d.
- (license license:gpl3+)))
+ ;; This includes the submodules greedy, c3d and digestible.
+ (license license:gpl3+))))
(define-public metapixel
;; Follow stable branch.
D gnu/packages/patches/itk-snap-alt-glibc-compat.patch => gnu/packages/patches/itk-snap-alt-glibc-compat.patch +0 -22
@@ 1,22 0,0 @@
-Retrieved from ALT Linux.
-https://git.altlinux.org/tasks/273587/build/300/x86_64/srpm/itk-snap-3.8.0-alt6.src.rpm
-
-diff --git a/GUI/Qt/main.cxx b/GUI/Qt/main.cxx
-index 576f7160..ceab92e6 100644
---- a/GUI/Qt/main.cxx
-+++ b/GUI/Qt/main.cxx
-@@ -51,12 +51,13 @@ using namespace std;
- #if defined (__unix__) || (defined (__APPLE__) && defined (__MACH__))
-
- #include <signal.h>
-+#include <string.h>
- #include <execinfo.h>
-
- void SegmentationFaultHandler(int sig)
- {
- cerr << "*************************************" << endl;
-- cerr << "ITK-SNAP: " << sys_siglist[sig] << endl;
-+ cerr << "ITK-SNAP: " << strsignal(sig) << " (" << sigabbrev_np(sig) << ")" << endl;
- cerr << "BACKTRACE: " << endl;
- void *array[50];
- int nsize = backtrace(array, 50);