diff options
Diffstat (limited to 'gnu/packages/image-processing.scm')
| -rw-r--r-- | gnu/packages/image-processing.scm | 433 |
1 files changed, 414 insertions, 19 deletions
diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-processing.scm index a8f40c4454..70c820e76b 100644 --- a/gnu/packages/image-processing.scm +++ b/gnu/packages/image-processing.scm @@ -21,6 +21,7 @@ ;;; Copyright © 2021 Ivan Gankevich <[email protected]> ;;; Copyright © 2022 Maxim Cournoyer <[email protected]> ;;; Copyright © 2022 Tomasz Jeneralczyk <[email protected]> +;;; Copyright © 2022 Paul A. Patience <[email protected]> ;;; ;;; This file is part of GNU Guix. ;;; @@ -54,11 +55,14 @@ #:use-module (gnu packages boost) #:use-module (gnu packages check) #:use-module (gnu packages compression) + #:use-module (gnu packages cpp) #:use-module (gnu packages curl) #:use-module (gnu packages docbook) #:use-module (gnu packages documentation) #:use-module (gnu packages flex) #:use-module (gnu packages fontutils) + #:use-module (gnu packages game-development) + #:use-module (gnu packages gcc) #:use-module (gnu packages geo) #:use-module (gnu packages ghostscript) #:use-module (gnu packages gimp) @@ -74,18 +78,24 @@ #:use-module (gnu packages imagemagick) #:use-module (gnu packages linux) #:use-module (gnu packages maths) + #:use-module (gnu packages mpi) #:use-module (gnu packages pdf) #:use-module (gnu packages perl) #:use-module (gnu packages photo) #:use-module (gnu packages pkg-config) + #:use-module (gnu packages pretty-print) #:use-module (gnu packages protobuf) #:use-module (gnu packages python) #:use-module (gnu packages python-check) + #:use-module (gnu packages python-science) #:use-module (gnu packages python-xyz) #:use-module (gnu packages qt) + #:use-module (gnu packages sdl) #:use-module (gnu packages serialization) + #:use-module (gnu packages sphinx) #:use-module (gnu packages sqlite) #:use-module (gnu packages tbb) + #:use-module (gnu packages textutils) #:use-module (gnu packages tls) #:use-module (gnu packages version-control) #:use-module (gnu packages video) @@ -99,26 +109,29 @@ (define-public bart (package (name "bart") - (version "0.7.00") + (version "0.8.00") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/mrirecon/bart") - (commit "d1b0e576c3f759089915565d5bf57832acf7b03e"))) + (commit "eacc67b95cf128487ecc48f0e6541ea4dca08818"))) (file-name (git-file-name name version)) (sha256 - (base32 "159rj3agr9pb9lg38b56rnw3d8wcbkmb2n718z26zpy4c6a6d9rn")))) + (base32 "05lcf7c3g7ms5h82bw1mi4kzkdv5wpqi1zrfhqfkgbcpd3irj6aq")))) (build-system gnu-build-system) (arguments (list #:test-target "utest" #:make-flags #~(list (string-append "PREFIX=" #$output) + "PARALLEL=1" + "PARALLEL_NJOBS=1" "OPENBLAS=1" "SCALAPACK=1" (string-append "BLAS_BASE=" #$(this-package-input "openblas")) (string-append "FFTW_BASE=" #$(this-package-input "fftw"))) + #:parallel-build? #false ;leads to non-deterministic output #:phases #~(modify-phases %standard-phases (delete 'configure) @@ -196,7 +209,9 @@ licences similar to the Modified BSD licence.")))) (base32 "0qpcd3n26q52dpyibm11f5l6cgscdr54p2jish39gc3p1f5h3ws1")) (patches (search-patches "mia-fix-boost-headers.patch" - "mia-vtk9.patch")))) + "mia-vtk9.patch" + "mia-vtk92.patch" + "mia-vtk-version.patch")))) (build-system cmake-build-system) (arguments `(#:configure-flags @@ -309,7 +324,7 @@ many popular formats.") (define-public vtk (package (name "vtk") - (version "9.0.1") + (version "9.2.2") (source (origin (method url-fetch) (uri (string-append "https://vtk.org/files/release/" @@ -317,9 +332,7 @@ many popular formats.") "/VTK-" version ".tar.gz")) (sha256 (base32 - "1ir2lq9i45ls374lcmjzw0nrm5l5hnm1w47lg8g8d0n2j7hsaf8v")) - (patches - (search-patches "vtk-fix-freetypetools-build-failure.patch")) + "0x8h2bwxq2870067j7wqd0qym87pa3inkbri93zrdb0zwwmhlnqw")) (modules '((guix build utils))) (snippet '(begin @@ -368,14 +381,6 @@ many popular formats.") "-DVTK_WRAP_PYTHON=ON" "-DVTK_PYTHON_VERSION:STRING=3" ) - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-sources - (lambda _ - (substitute* "Common/Core/vtkFloatingPointExceptions.cxx" - (("<fenv.h>") "<cfenv>")) - (substitute* "Common/Core/CMakeLists.txt" - (("fenv.h") "cfenv"))))) #:tests? #f)) ;XXX: test data not included (inputs (list double-conversion @@ -623,7 +628,7 @@ integrates with various databases on GUI toolkits such as Qt and Tk.") (sha256 (base32 "0ga0l4ranp1834gxgp487ll1amvmssa02l2nk5ja5w0rx4d8hh26")))))) (inputs - (list ffmpeg + (list ffmpeg-4 gtk+ gtkglext hdf5 @@ -671,7 +676,7 @@ things like: (define-public vips (package (name "vips") - (version "8.10.6") + (version "8.13.1") (source (origin (method url-fetch) @@ -679,7 +684,7 @@ things like: "https://github.com/libvips/libvips/releases/download/v" version "/vips-" version ".tar.gz")) (sha256 - (base32 "0vjsh3i0861f6h9as3bch956cidz824zz499pvhjs3lfjn6hhs14")))) + (base32 "00kp3439jcqv9l2gcjg88xzvlq8clv54z1m3x66i3chvarz7ndxd")))) (build-system gnu-build-system) (native-inputs (list gobject-introspection pkg-config)) @@ -868,6 +873,368 @@ create a set of formula connecting your objects together, and on a change nip2 recalculates.") (license license:gpl2+))) +;; This package bundles and extends VTK. It also reuses the VTK build system +;; to some degree. Sadly, it does not seem to be possible to build with an +;; external VTK, despite the CMake option PARAVIEW_USE_EXTERNAL_VTK. +(define-public paraview-5.9 + (package + (name "paraview") + (version "5.9.1") + (source + (origin + (method url-fetch) + (uri (string-append "https://www.paraview.org/files/v" + (version-major+minor version) + "/ParaView-v" version ".tar.xz")) + (sha256 + (base32 "13aczmfshzia324h9r2m675yyrklz2308rf98n444ppmzfv6qj0d")))) + (build-system qt-build-system) + (arguments + (list + #:build-type "Release" ;Build without debug symbols to save space + #:configure-flags + '(list "-DPARAVIEW_BUILD_WITH_EXTERNAL=ON" + "-DPARAVIEW_BUILD_SHARED_LIBS=ON" + "-DPARAVIEW_BUILD_DEVELOPER_DOCUMENTATION=OFF" + "-DPARAVIEW_USE_PYTHON=ON" + "-DPARAVIEW_ENABLE_FFMPEG=ON" + "-DPARAVIEW_ENABLE_GDAL=ON" + "-DPARAVIEW_ENABLE_WEB=OFF" + + "-DVTK_MODULE_USE_EXTERNAL_VTK_doubleconversion=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_eigen=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_expat=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_freetype=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_gl2ps=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_glew=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_hdf5=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_jpeg=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_libxml2=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_lz4=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_lzma=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_netcdf=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_png=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_theora=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_tiff=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_utf8=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_zlib=ON" + + "-DVTK_MODULE_USE_EXTERNAL_ParaView_vtkcatalyst=OFF" + "-DVTK_MODULE_USE_EXTERNAL_VTK_cgns=OFF" + "-DVTK_MODULE_USE_EXTERNAL_VTK_exprtk=OFF" + "-DVTK_MODULE_USE_EXTERNAL_VTK_fmt=OFF" + "-DVTK_MODULE_USE_EXTERNAL_VTK_ioss=OFF"))) + (inputs + (list ;; XXX: We can't simply #:use-module due to a cycle somewhere. + (module-ref + (resolve-interface '(gnu packages engineering)) + 'cgns) + cli11 + double-conversion + eigen + expat + ffmpeg-4 + freetype + gdal + gl2ps + glew + hdf5 + jsoncpp + libharu + libjpeg-turbo + libpng + libtheora + libtiff + libxml2 + lz4 + mesa + netcdf + protobuf + pugixml + python + qtbase-5 + qtsvg-5 + qttools-5 + qtxmlpatterns + utfcpp + zlib)) + (home-page "https://www.paraview.org/") + (synopsis "Data analysis and visualization application") + (description "ParaView is a data analysis and visualization application. +Users can quickly build visualizations to analyze their data using qualitative +and quantitative techniques. The data exploration can be done interactively +in 3D or programmatically using ParaView’s batch processing capabilities.") + (license license:bsd-3))) + +(define-public paraview + (package + (name "paraview") + (version "5.11.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.kitware.com/paraview/paraview.git") + (commit (string-append "v" version)) + (recursive? #t))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0qifzsbgg8f7zvg5a4934nql6nv5b6sm1f59bylyc6v5bqd0myas")) + (modules '((guix build utils))) + (snippet + ;; TODO: Also remove unused bundled libraries and plugins? + #~(begin + ;; Remove bundled ParaView libraries which are available in Guix + ;; or undesired. + (for-each (lambda (dir) + (delete-file-recursively + (string-append "ThirdParty/" dir "/vtk" + (string-downcase dir)))) + '(;;"CosmoHaloFinder" + ;;"IceT" + "NvPipe" ; Don't want NvPipe support + ;;"QtTesting" + ;;"cinema" + ;;"cinemasci" + "protobuf")) + ;; Remove undesired ParaView plugins. + (delete-file-recursively "Plugins/pvNVIDIAIndeX") + ;; Remove bundled VTK libraries which are available in Guix. + (for-each (lambda (dir) + (delete-file-recursively + (string-append "VTK/ThirdParty/" dir "/vtk" dir))) + '(;;"cgns" + "cli11" + ;;"diy2" + "doubleconversion" + "eigen" + ;;"exodusII" + "expat" + ;;"exprtk" + ;;"fides" + "fmt" + "freetype" + "gl2ps" + "glew" + ;;"h5part" + "hdf5" + ;;"ioss" + "jpeg" + "jsoncpp" + ;;"kissfft" + ;;"libharu" ; Requires some PRs applied to 2.3.0 + "libproj" + "libxml2" + ;;"loguru" + "lz4" + "lzma" + "mpi4py" + "netcdf" + ;;"nlohmannjson" ; ParFlow build fails even with bundled + "ogg" + ;;"pegtl" + "png" + "pugixml" + "sqlite" + "theora" + "tiff" + "utf8" + ;;"verdict" + ;;"vpic" + ;;"vtkm" + ;;"xdmf2" + ;;"xdmf3" + ;;"zfp" + "zlib")))))) + (build-system qt-build-system) + (arguments + (list + #:build-type "Release" ; 542 MiB in release mode + #:tests? #f ; Downloads test data + #:configure-flags + #~(let ((doc (string-append #$output "/share/doc/" #$name "-" #$version))) + (list + (string-append "-DCMAKE_INSTALL_DOCDIR=" doc) ; For paraview.qch + + ;; ParaView build options + "-DPARAVIEW_BUILD_DEVELOPER_DOCUMENTATION=ON" + (string-append "-DPARAVIEW_GENERATED_DOCUMENTATION_OUTPUT_DIRECTORY=" doc) + + ;; ParaView capability options + ;;"-DPARAVIEW_USE_EXTERNAL_VTK=ON" ; Unsupported by ParaView + "-DPARAVIEW_USE_MPI=ON" + "-DPARAVIEW_USE_PYTHON=ON" + "-DPARAVIEW_USE_QTWEBENGINE=ON" + + ;; ParaView features + ;; + ;; Enable those that are disabled by default. + ;; Commented means the dependencies are missing from Guix + ;; (or are otherwise described). + ;;"-DPARAVIEW_ENABLE_ADIOS2=ON" + ;;"-DPARAVIEW_ENABLE_COSMOTOOLS=ON" + ;;"-DPARAVIEW_ENABLE_CATALYST=ON" + "-DPARAVIEW_ENABLE_FFMPEG=ON" + ;;"-DPARAVIEW_ENABLE_FIDES=ON" + "-DPARAVIEW_ENABLE_GDAL=ON" + ;;"-DPARAVIEW_ENABLE_LAS=ON" + ;;"-DPARAVIEW_ENABLE_LOOKINGGLASS=ON" ; Downloads dependency + ;;"-DPARAVIEW_ENABLE_MOMENTINVARIANTS=ON" ; Downloads dependency + "-DPARAVIEW_ENABLE_MOTIONFX=ON" + ;;"-DPARAVIEW_ENABLE_OPENTURNS=ON" + ;;"-DPARAVIEW_ENABLE_OPENVDB=ON" ; Dependency not found + ;;"-DPARAVIEW_ENABLE_PDAL=ON" + ;;"-DPARAVIEW_ENABLE_RAYTRACING=ON" + "-DPARAVIEW_ENABLE_VISITBRIDGE=ON" + "-DPARAVIEW_ENABLE_XDMF3=ON" + + ;; ParaView miscellaneous options + ;; + ;; Without -DPARAVIEW_DATA_EXCLUDE_FROM_ALL=OFF, test data is + ;; downloaded even with tests disabled. + "-DPARAVIEW_VERSIONED_INSTALL=OFF" + "-DPARAVIEW_DATA_EXCLUDE_FROM_ALL=OFF" + + ;; ParaView plugins + ;; + ;; Enable those that are disabled by default. + ;; Commented means the dependencies are missing from Guix + ;; (or are otherwise described). + ;;"-DPARAVIEW_PLUGIN_ENABLE_AdiosReaderPixie=ON" + ;;"-DPARAVIEW_PLUGIN_ENABLE_AdiosReaderStaging=ON" + "-DPARAVIEW_PLUGIN_ENABLE_CAVEInteraction=ON" + ;;"-DPARAVIEW_PLUGIN_ENABLE_CDIReader=ON" + "-DPARAVIEW_PLUGIN_ENABLE_GeographicalMap=ON" + "-DPARAVIEW_PLUGIN_ENABLE_GmshIO=ON" + "-DPARAVIEW_PLUGIN_ENABLE_InSituExodus=ON" + ;;"-DPARAVIEW_PLUGIN_ENABLE_LookingGlass=ON" + "-DPARAVIEW_PLUGIN_ENABLE_NetCDFTimeAnnotationPlugin=ON" + ;;"-DPARAVIEW_PLUGIN_ENABLE_ParFlow=ON" ; Build fails + ;;"-DPARAVIEW_PLUGIN_ENABLE_PythonQtPlugin=ON" + "-DPARAVIEW_PLUGIN_ENABLE_SpaceMouseInteractor=ON" + ;;"-DPARAVIEW_PLUGIN_ENABLE_VDFReaderPlugin=ON" + ;;"-DPARAVIEW_PLUGIN_ENABLE_XRInterface=ON" ; Build fails + ;;"-DPARAVIEW_PLUGIN_ENABLE_zSpace=ON" + + ;; VTK options + "-DVTK_SMP_IMPLEMENTATION_TYPE=TBB" + "-DVTKm_ENABLE_MPI=ON" + + ;; External libraries for ParaView and VTK + "-DVTK_MODULE_USE_EXTERNAL_ParaView_protobuf=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_cli11=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_doubleconversion=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_eigen=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_expat=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_fmt=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_freetype=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_gl2ps=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_glew=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_hdf5=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_jpeg=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_jsoncpp=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_libproj=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_libxml2=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_lz4=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_lzma=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_mpi4py=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_netcdf=ON" + ;;"-DVTK_MODULE_USE_EXTERNAL_VTK_nlohmannjson=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_ogg=ON" + ;;"-DVTK_MODULE_USE_EXTERNAL_VTK_pegtl=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_png=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_pugixml=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_sqlite=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_theora=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_tiff=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_utf8=ON" + "-DVTK_MODULE_USE_EXTERNAL_VTK_zlib=ON")) + #:phases + #~(modify-phases %standard-phases + (add-after 'set-paths 'hide-gfortran + (lambda _ + (setenv "CPLUS_INCLUDE_PATH" + (string-join + (delete (string-append #$(this-package-native-input "gfortran") + "/include/c++") + (string-split (getenv "CPLUS_INCLUDE_PATH") #\:)) + ":")))) + (replace 'install-license-files + (lambda _ + (let ((src (string-append #$output "/share/licenses/ParaView")) + (dst (string-append #$output "/share/doc/" + #$name "-" #$version "/licenses"))) + (copy-recursively src dst) + (delete-file-recursively (dirname src)))))))) + (native-inputs + (list gfortran + ;; For the documentation + doxygen + graphviz + perl + python-sphinx)) + (inputs + (list boost + cli11 + curl + double-conversion + eigen + expat + ffmpeg + fmt + freetype + gdal + gl2ps + glew + gmsh + hdf5 + ;;json-modern-cxx ;For ParFlow; build fails + jsoncpp + libjpeg-turbo + libogg + libpng + libtheora + libtiff + libxcursor + libxml2 + libxt + lz4 + lzip + mesa + netcdf + openmpi + ;;openvdb ;For OpenVDB; dependency not found + ;;openvr ;For XRInterface; build fails + ;;pegtl ;For VTK; build fails + proj + protobuf + pugixml + python-cftime + python-matplotlib + python-mpi4py + python-numpy + python-wrapper + qtbase-5 + qtdeclarative-5 + qtmultimedia-5 + qtsvg-5 + qttools-5 + qtwebchannel-5 + qtwebengine-5 + qtx11extras + qtxmlpatterns + sdl2 + sqlite + tbb + utfcpp + zlib)) + (home-page "https://www.paraview.org/") + (synopsis "VTK-based, parallel data analyzer and visualizer") + (description "ParaView is a VTK-based, parallel data analyzer and +visualizer which allows exploring data interactively in 3D or +programmatically.") + (license license:bsd-3))) + (define-public vxl (package (name "vxl") @@ -1381,3 +1748,31 @@ segmentation.") "Image and video labeling tool supporting different shapes like polygons, rectangles, circles, lines, points and VOC/COCO export.") (license license:gpl3+))) + +(define-public charls + (package + (name "charls") + (version "2.3.4") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/team-charls/charls/") + (commit (string-append version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0g3f1rfimk30rqmi7ic4i5vfphyqbbpsyyhwqq1iss9wjwaz2vs5")))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags '("-DCMAKE_BUILD_TYPE:STRING=Release" + "-DBUILD_SHARED_LIBS=On"))) + (native-inputs (list git pkg-config)) + (home-page "https://github.com/team-charls/charls") + (synopsis "Library for using JPEG-LS compliant images") + (description + "CharLS is a codec library that can be used to build applications that +can handle JPEG-LS compliant images. In the application you are writing you +can call the CharLS codec and pass it images (sometimes called raster bitmaps), + to have them encoded to JPEG-LS, or JPEG-LS streams, which CharLS will decode +to images.") + (license license:bsd-3))) |