diff options
Diffstat (limited to 'gnu/packages/image-processing.scm')
| -rw-r--r-- | gnu/packages/image-processing.scm | 139 |
1 files changed, 73 insertions, 66 deletions
diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-processing.scm index 1995f71cc2..f4bf1724b4 100644 --- a/gnu/packages/image-processing.scm +++ b/gnu/packages/image-processing.scm @@ -19,6 +19,7 @@ ;;; Copyright © 2021 Paul Garlick <pgarlick@tourbillion-technology.com> ;;; Copyright © 2021 Guillaume Le Vaillant <glv@posteo.net> ;;; Copyright © 2021 Ivan Gankevich <i.gankevich@spbu.ru> +;;; Copyright © 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -145,7 +146,7 @@ Magnetic Resonance Imaging.") (define-public dcmtk (package (name "dcmtk") - (version "3.6.6") + (version "3.6.7") (source (origin (method url-fetch) @@ -154,8 +155,11 @@ Magnetic Resonance Imaging.") "dcmtk" (string-join (string-split version #\.) "") "/dcmtk-" version ".tar.gz")) (sha256 - (base32 "13j5yf3p6qj3mr17d77r3kcqchf055hgvk1w15vmdr8f54mwcnb8")))) + (base32 "02kix73qhndgb56cmi5327666i6imp7hi17wwqp26q4d7s72jn3w")))) (build-system cmake-build-system) + (arguments + ;; By default, only static archives are built. + (list #:configure-flags #~(list "-DBUILD_SHARED_LIBS=ON"))) (inputs (list icu4c libjpeg-turbo @@ -181,7 +185,7 @@ licences similar to the Modified BSD licence.")))) (define-public mia (package (name "mia") - (version "2.4.6") + (version "2.4.7") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/mia/mia/" @@ -189,37 +193,41 @@ licences similar to the Modified BSD licence.")))) "/mia-" version ".tar.xz")) (sha256 (base32 - "0j4nd5z7i3v199jh7hqqhwd4g7snchizkc7rhzanpvngqg91m1pb")))) + "0qpcd3n26q52dpyibm11f5l6cgscdr54p2jish39gc3p1f5h3ws1")) + (patches (search-patches "mia-fix-boost-headers.patch")))) (build-system cmake-build-system) (arguments `(#:configure-flags - (list "-DMIA_CREATE_NIPYPE_INTERFACES=0" + (list "-DMIA_CREATE_NIPYPE_INTERFACES=OFF" "-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-turbo) - ("libpng" ,libpng) - ("libtiff" ,libtiff) - ("libxml" ,libxml2) - ("libxml++" ,libxml++) - ("maxflow" ,maxflow) - ("niftilib" ,niftilib) - ("nlopt" ,nlopt) - ("openexr" ,openexr-2) - ("python-lxml" ,python2-lxml) - ("vtk" ,vtk))) + (list boost + dcmtk + doxygen + eigen + fftw + fftwf + gsl + gts + hdf5 + itpp + libjpeg-turbo + libpng + libtiff + libxml2 + libxml++ + maxflow + niftilib + nlopt + openexr-2 + python-lxml + ;; The build fails when using the regular VTK (currently at version + ;; 9), with error "addons/vtk/vtkvf.cc:23:10: fatal error: + ;; vtkStructuredPointsReader.h: No such file or directory". + vtk-7)) (native-inputs - `(("pkg-config" ,pkg-config) - ("python" ,python-2))) + (list pkg-config + python-wrapper)) (home-page "http://mia.sourceforge.net") (synopsis "Toolkit for gray scale medical image analysis") (description "MIA provides a combination of command line tools, plug-ins, @@ -407,10 +415,10 @@ a suite of 3D interaction widgets, supports parallel processing, and integrates with various databases on GUI toolkits such as Qt and Tk.") (license license:bsd-3))) -;; itksnap needs an older variant of VTK. -(define-public vtk-6 - (package (inherit vtk) - (version "6.3.0") +(define-public vtk-7 + (package + (inherit vtk) + (version "7.1.1") (source (origin (method url-fetch) (uri (string-append "https://vtk.org/files/release/" @@ -418,11 +426,16 @@ integrates with various databases on GUI toolkits such as Qt and Tk.") "/VTK-" version ".tar.gz")) (sha256 (base32 - "0pla1r5mvkgl4sl213gfdhzrypdgai0h3z5mfgm6p9jz9hsr794j")))) - (inputs - (modify-inputs (package-inputs vtk) - (replace "jsoncpp" jsoncpp-for-tensorflow) - (replace "python" python-2))))) ;fails to build with Python 3.9 + "0nm7xwwj7rnsxjdv2ssviys8nhci4n9iiiqm2y14s520hl2dsp1d")) + (patches (search-patches "vtk-7-python-compat.patch" + "vtk-7-hdf5-compat.patch" + "vtk-7-gcc-10-compat.patch")))) + (arguments + (substitute-keyword-arguments (package-arguments vtk) + ((#:configure-flags flags) + ;; Otherwise, the build would fail with: "error: invalid conversion + ;; from ‘const char*’ to ‘char*’ [-fpermissive]". + `(cons "-DCMAKE_CXX_FLAGS=-fpermissive" ,flags)))))) (define-public opencv (package @@ -1010,7 +1023,8 @@ combine the information contained in both.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "15i5ixpryfrbf3vrrb5rici8fb585f25k0v1ljds16bp1f1msr4q")))) + (base32 "15i5ixpryfrbf3vrrb5rici8fb585f25k0v1ljds16bp1f1msr4q")) + (patches (search-patches "itk-snap-alt-glibc-compat.patch")))) (build-system cmake-build-system) (arguments `(#:configure-flags @@ -1029,22 +1043,19 @@ combine the information contained in both.") (substitute* "CMakeLists.txt" (("install_qt5_executable\ \\(\\$\\{SNAP_MAIN_INSTALL_DIR\\}/\\$\\{SNAP_EXE\\}\\)") - "")) - #t)) + "")))) (add-after 'unpack 'disable-gui-tests (lambda _ ;; The GUI tests just time out. (substitute* "CMakeLists.txt" ((" (Workspace|DiffSpace|ProbeIntensity|RegionCompetition\ |RandomForest|RandomForestBailOut)") - "")) - #t)) + "")))) (add-after 'unpack 'make-reproducible (lambda _ (substitute* "CMakeLists.txt" (("TODAY\\(SNAP_VERSION_COMPILE_DATE\\)") - "SET(SNAP_VERSION_COMPILE_DATE \"(removed for reproducibility)\")")) - #t)) + "SET(SNAP_VERSION_COMPILE_DATE \"(removed for reproducibility)\")")))) (add-after 'unpack 'prepare-submodules (lambda* (#:key inputs #:allow-other-keys) (rmdir "Submodules/c3d") @@ -1055,19 +1066,16 @@ combine the information contained in both.") (("vcl_") "std::")) (rmdir "Submodules/greedy") (symlink (assoc-ref inputs "greedy-src") - "Submodules/greedy") - #t)) + "Submodules/greedy"))) (add-after 'unpack 'fix-includes (lambda _ (substitute* "GUI/Model/RegistrationModel.cxx" (("<vnl_symmetric_eigensystem.h>") - "<vnl/algo/vnl_symmetric_eigensystem.h>")) - #t)) + "<vnl/algo/vnl_symmetric_eigensystem.h>")))) (add-before 'check 'prepare-tests (lambda _ ;; Needed by at least one test. - (setenv "HOME" "/tmp") - #t)) + (setenv "HOME" "/tmp"))) (add-after 'install 'wrap-executable (lambda* (#:key inputs outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) @@ -1076,23 +1084,22 @@ combine the information contained in both.") ,(map (lambda (label) (string-append (assoc-ref inputs label) "/lib/qt5/plugins")) - '("qtbase" "qtdeclarative")))) - #t)))))) + '("qtbase" "qtdeclarative")))))))))) (inputs - `(("curl" ,curl) - ("fftw" ,fftw) - ("fftwf" ,fftwf) - ("glu" ,glu) - ("hdf5" ,hdf5) - ("mesa" ,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. - ("itk" ,insight-toolkit-4.12) - ("vtk" ,vtk-6) - ("qtbase" ,qtbase-5) - ("qtdeclarative" ,qtdeclarative) - ("vxl" ,vxl-1) - ("zlib" ,zlib))) + (list curl + fftw + fftwf + glu + hdf5 + 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 + vxl-1 + zlib)) (native-inputs `(("googletest" ,googletest) ("qttools" ,qttools) |