diff options
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/local.mk | 1 | ||||
| -rw-r--r-- | gnu/packages/image-processing.scm | 215 | ||||
| -rw-r--r-- | gnu/packages/patches/itk-snap-alt-glibc-compat.patch | 22 |
3 files changed, 105 insertions, 133 deletions
diff --git a/gnu/local.mk b/gnu/local.mk index 17375a2903..f51bc26cdb 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -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 \ diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-processing.scm index db792a62fc..d6987b367a 100644 --- a/gnu/packages/image-processing.scm +++ b/gnu/packages/image-processing.scm @@ -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. diff --git a/gnu/packages/patches/itk-snap-alt-glibc-compat.patch b/gnu/packages/patches/itk-snap-alt-glibc-compat.patch deleted file mode 100644 index 764c5da2c2..0000000000 --- a/gnu/packages/patches/itk-snap-alt-glibc-compat.patch +++ /dev/null @@ -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); |