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guix/gnu/packages/image-processing.scm
Vinicius Monego 5312f34f70
gnu: gmic: Update to 3.4.1. 
* gnu/packages/image-processing.scm (gmic): Update to 3.4.1.

Change-Id: I8c758f27fa21b497b8c1493c309bdf4cf709c0cc
2024-09-02 17:42:34 -03:00

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;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2017 John Darrington <jmd@gnu.org>
;;; Copyright © 2017, 2019, 2022, 2024 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2014, 2021-2023 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2014 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2018–2021 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
;;; Copyright © 2018 Lprndn <guix@lprndn.info>
;;; Copyright © 2019, 2021, 2023 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
;;; Copyright © 2020, 2021, 2024 Vinicius Monego <monego@posteo.net>
;;; Copyright © 2020 Pierre Neidhardt <mail@ambrevar.xyz>
;;; Copyright © 2020 Brendan Tildesley <mail@brendan.scot>
;;; Copyright © 2021 Oleh Malyi <astroclubzp@gmail.com>
;;; Copyright © 2021, 2022, 2024 Felix Gruber <felgru@posteo.net>
;;; Copyright © 2021 Andy Tai <atai@atai.org>
;;; Copyright © 2021 Ekaitz Zarraga <ekaitz@elenq.tech>
;;; 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>
;;; Copyright © 2022 Tomasz Jeneralczyk <tj@schwi.pl>
;;; Copyright © 2022 Paul A. Patience <paul@apatience.com>
;;; Copyright © 2023 Cairn <cairn@pm.me>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (gnu packages image-processing)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix gexp)
#:use-module (guix utils)
#:use-module (guix download)
#:use-module (guix git-download)
#:use-module (guix build-system qt)
#:use-module (guix build-system cmake)
#:use-module (guix build-system gnu)
#:use-module (guix build-system python)
#:use-module (guix build-system pyproject)
#:use-module (gnu packages)
#:use-module (gnu packages algebra)
#:use-module (gnu packages base)
#:use-module (gnu packages bash)
#:use-module (gnu packages bison)
#: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 gd)
#:use-module (gnu packages geo)
#:use-module (gnu packages ghostscript)
#:use-module (gnu packages gimp)
#:use-module (gnu packages gl)
#:use-module (gnu packages glib)
#:use-module (gnu packages gnome)
#:use-module (gnu packages graphics)
#:use-module (gnu packages graphviz)
#:use-module (gnu packages gstreamer)
#:use-module (gnu packages gtk)
#:use-module (gnu packages icu4c)
#:use-module (gnu packages image)
#:use-module (gnu packages imagemagick)
#:use-module (gnu packages linux)
#:use-module (gnu packages maths)
#:use-module (gnu packages mpi)
#:use-module (gnu packages opencl)
#: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-build)
#: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 swig)
#: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)
#:use-module (gnu packages xiph)
#:use-module (gnu packages xml)
#:use-module (gnu packages xorg)
#:use-module (ice-9 match)
#:use-module (srfi srfi-1))
;; TODO: this is not reproducible.
(define-public bart
(package
(name "bart")
(version "0.8.00")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/mrirecon/bart")
(commit "eacc67b95cf128487ecc48f0e6541ea4dca08818")))
(file-name (git-file-name name version))
(sha256
(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)
(add-after 'unpack 'patch-/bin/bash
(lambda _
(substitute* "tests/pics.mk"
(("/bin/bash") (which "bash"))))))))
(inputs
(list fftw
fftwf
libpng
openblas
python
scalapack))
(native-inputs
(list doxygen
util-linux)) ;for flock
(home-page "https://mrirecon.github.io/bart/")
(synopsis "Toolbox for computational magnetic resonance imaging")
(description "The Berkeley Advanced Reconstruction Toolbox (BART) is an
image-reconstruction framework for Computational Magnetic Resonance Imaging.
The tools in this software implement various reconstruction algorithms for
Magnetic Resonance Imaging.")
(license license:bsd-3)))
(define-public dcmtk
(package
(name "dcmtk")
(version "3.6.8")
(source
(origin
(method url-fetch)
(uri
(string-append "ftp://dicom.offis.de/pub/dicom/offis/software/dcmtk/"
"dcmtk" (string-join (string-split version #\.) "")
"/dcmtk-" version ".tar.gz"))
(sha256
(base32 "03vjv2lq5kr79ghf8v0q9wskkrcr2ygi097nybmqs4q3amjpc813"))))
(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
libpng
libtiff
libxml2
openssl
zlib))
(native-inputs
(list doxygen)) ; for HTML documentation
(home-page "https://dcmtk.org")
(synopsis "Libraries and programs implementing parts of the DICOM standard")
(description "DCMTK is a collection of libraries and applications
implementing large parts the DICOM standard. It includes software for
examining, constructing and converting DICOM image files, handling offline
media, sending and receiving images over a network connection, as well as
demonstrative image storage and worklist servers.")
(license (license:fsf-free
"file://COPYRIGHT"
"A union of the Apache 2.0 licence and various non-copyleft
licences similar to the Modified BSD licence."))))
(define-public mia
(package
(name "mia")
(version "2.4.7")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/mia/mia/"
(version-major+minor version)
"/mia-" version ".tar.xz"))
(sha256
(base32
"0qpcd3n26q52dpyibm11f5l6cgscdr54p2jish39gc3p1f5h3ws1"))
(patches (search-patches "mia-fix-boost-headers.patch"
"mia-vtk9.patch"
"mia-vtk92.patch"
"mia-vtk-version.patch"))))
(build-system cmake-build-system)
(arguments
`(#:configure-flags
(list "-DMIA_CREATE_NIPYPE_INTERFACES=OFF"
"-DCMAKE_CXX_FLAGS=-fpermissive")))
(inputs
(list boost
dcmtk
doxygen
eigen
fftw
fftwf
gsl
gts
hdf5
itpp
libjpeg-turbo
libpng
libtiff
libxml2
libxml++
maxflow
niftilib
nlopt
openexr-2
python-lxml
vtk))
(native-inputs
(list pkg-config
python-wrapper))
(home-page "https://mia.sourceforge.net")
(synopsis "Toolkit for gray scale medical image analysis")
(description "MIA provides a combination of command line tools, plug-ins,
and libraries that make it possible run image processing tasks interactively
in a command shell and to prototype using the shell's scripting language. It
is built around a plug-in structure that makes it easy to add functionality
without compromising the original code base and it makes use of a wide variety
of external libraries that provide additional functionality.")
(license license:gpl3+)))
(define-public opencolorio
(package
(name "opencolorio")
(version "2.3.2")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/AcademySoftwareFoundation/OpenColorIO")
(commit (string-append "v" version))))
(sha256
(base32 "1h33s2pfy28nj836kx6xx3iks7v38g3kx7c4f6zn1dpskl0zf809"))
(file-name (git-file-name name version))))
(build-system cmake-build-system)
(arguments
;; XXX: GPU tests are failing.
(list #:configure-flags #~(list "-DOCIO_BUILD_GPU_TESTS=false")
#:phases #~(modify-phases %standard-phases
(add-after 'install 'fix-OpenColorIOConfig
(lambda _
;; Work around a CMake Zlib-detection bug:
;; https://gitlab.kitware.com/cmake/cmake/-/issues/25200
;; make OpenColorIOConfig.cmake is a normal cmake file
(substitute*
(string-append #$output
"/lib/cmake/OpenColorIO/OpenColorIOConfig.cmake")
(("\\.#define ZLIB_VERSION \"1\\.3\"")
"")))))))
(native-inputs
;; XXX: OCIO has unit tests for OpenShadingLanguage, but they fail.
;; They also require OIIO, but OCIO is an optional dependency to it.
(list pybind11-2.10 python-wrapper))
(inputs
(list expat
freeglut
glew
imath
lcms
libglvnd
minizip-ng
openexr
pystring
yaml-cpp
zlib))
(home-page "https://opencolorio.org")
(synopsis "Color management for visual effects and animation")
(description
"OpenColorIO, or OCIO, is a complete color management solution geared
towards motion picture production, with an emphasis on visual effects and
computer animation. It provides a straightforward and consistent user
experience across all supporting applications while allowing for sophisticated
back-end configuration options suitable for high-end production usage.
OCIO is compatible with the @acronym{ACES, Academy Color Encoding
Specification} and is @acronym{LUT, look-up table}-format agnostic, supporting
many popular formats.")
(license license:bsd-3)))
(define-public vtk
(package
(name "vtk")
(version "9.3.0")
(source (origin
(method url-fetch)
(uri (string-append "https://vtk.org/files/release/"
(version-major+minor version)
"/VTK-" version ".tar.gz"))
(sha256
(base32
"1s8vd34nhrgnw1bf9zhfn062d53fwq3csjfwvm7lxcr5a8lvkizx"))
(modules '((guix build utils)))
(snippet
'(begin
(for-each
(lambda (dir)
(delete-file-recursively
(string-append "ThirdParty/" dir "/vtk" dir)))
;; pugixml depended upon unconditionally
'("doubleconversion" "eigen" "expat" "freetype" "gl2ps"
"glew" "hdf5" "jpeg" "jsoncpp" "libharu" "libproj"
"libxml2" "lz4" "netcdf" "ogg" "png" "sqlite" "theora"
"tiff" "zlib"))
(substitute* "IO/ExportPDF/vtkPDFContextDevice2D.cxx"
(("\\bHPDF_UINT16 (noPen|dash|dot|denseDot|dashDot|dashDotDot)\\b"
_ var)
(string-append "HPDF_REAL " var)))))))
(properties `((release-monitoring-url . "https://vtk.org/download/")))
(build-system cmake-build-system)
(arguments
(list #:build-type "Release" ;Build without '-g' to save space.
#:configure-flags
#~'( ;;"-DBUILD_TESTING:BOOL=TRUE" ;not honored
"-DVTK_USE_EXTERNAL=OFF" ;default
"-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_jsoncpp=ON"
"-DVTK_MODULE_USE_EXTERNAL_VTK_libharu=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_netcdf=ON"
"-DVTK_MODULE_USE_EXTERNAL_VTK_ogg=ON"
"-DVTK_MODULE_USE_EXTERNAL_VTK_png=ON"
;;"-DVTK_MODULE_USE_EXTERNAL_VTK_pugixml=ON" ;breaks IO/CityGML
"-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_zlib=ON"
"-DVTK_MODULE_ENABLE_VTK_RenderingExternal=YES" ;for F3D
"-DVTK_WRAP_PYTHON=ON"
"-DVTK_PYTHON_VERSION:STRING=3"
"-DVTK_SMP_ENABLE_OPENNMP=ON"
"-DVTK_SMP_ENABLE_TBB=ON"
"-DVTK_USE_MPI=ON"
#$@(if (target-riscv64?)
'("-DCMAKE_SHARED_LINKER_FLAGS=-latomic"
"-DCMAKE_EXE_LINKER_FLAGS=-latomic")
'()))
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'clear-reference-to-compiler
(lambda _
(define (choose . files)
(let loop ((files files))
(if (null? files)
#f
(if (file-exists? (car files))
(car files)
(loop (cdr files))))))
;; Do not retain a reference to GCC.
(substitute* (choose
"Common/Core/vtkBuild.h.in" ;dummy >=v9.3
"Common/Core/vtkConfigureDeprecated.h.in" ;v9.x
"Common/Core/vtkConfigure.h.in") ;v7.x
(("@CMAKE_CXX_COMPILER@") "c++")))))
#:tests? #f)) ;XXX: test data not included
(inputs
(list double-conversion
eigen
expat
freetype
gl2ps
glew
glu
hdf5
libharu
libjpeg-turbo
jsoncpp
libtheora
libx11
libxml2
libxt
lz4
mesa
netcdf
libpng
libtiff
openmpi
proj
python
;("pugixml" ,pugixml)
sqlite
xorgproto
zlib))
(propagated-inputs
;; VTK's 'VTK-vtk-module-find-packages.cmake' calls
;; 'find_package(THEORA)', which in turns looks for libogg. Likewise for
;; TBB.
(list libogg
tbb))
(home-page "https://vtk.org/")
(synopsis "Libraries for 3D computer graphics")
(description
"The Visualization Toolkit (VTK) is a C++ library for 3D computer graphics,
image processing and visualization. It supports a wide variety of
visualization algorithms including: scalar, vector, tensor, texture, and
volumetric methods; and advanced modeling techniques such as: implicit
modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay
triangulation. VTK has an extensive information visualization framework, has
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)))
(define-public vtk-7
(package
(inherit vtk)
(version "7.1.1")
(source (origin
(method url-fetch)
(uri (string-append "https://vtk.org/files/release/"
(version-major+minor version)
"/VTK-" version ".tar.gz"))
(sha256
(base32
"0nm7xwwj7rnsxjdv2ssviys8nhci4n9iiiqm2y14s520hl2dsp1d"))
(patches (search-patches "vtk-7-python-compat.patch"
"vtk-7-hdf5-compat.patch"
"vtk-7-gcc-10-compat.patch"
"vtk-7-gcc-11-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))
((#:phases phases)
#~(modify-phases #$phases
(add-after 'unpack 'remove-kernel-version
;; Avoid embedding the kernel version for reproducible builds
(lambda _
(substitute*
"ThirdParty/hdf5/vtkhdf5/config/cmake/libhdf5.settings.cmake.in"
(("Host system: \\@CMAKE_HOST_SYSTEM\\@")
"Host system: @CMAKE_SYSTEM_NAME@"))))))))))
(define-public opencv
(package
(name "opencv")
(version "4.10.0")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/opencv/opencv")
(commit version)))
(file-name (git-file-name name version))
(modules '((guix build utils)))
(snippet
'(begin
;; Remove external libraries. Almost all of them are
;; available in Guix.
(with-directory-excursion "3rdparty"
(for-each delete-file-recursively
'("carotene"
"cpufeatures"
"flatbuffers"
"ffmpeg"
"include"
"ippicv"
"ittnotify"
"libjasper"
"libjpeg"
"libjpeg-turbo"
"libpng"
"libtiff"
"libwebp"
"openexr"
"openjpeg"
"openvx"
"protobuf"
;;"quirc"
"tbb"
"zlib")))
;; Delete any bundled .jar files.
(for-each delete-file (find-files "." "\\.jar$"))))
(sha256
(base32
"0vinljqhq3r8sffy2396q688irb6iz389sv5vlg04z9y7mvddb8x"))))
(build-system cmake-build-system)
(arguments
`(#:configure-flags
(list "-DWITH_ADE=OFF" ;we don't have a package for ade yet
"-DWITH_IPP=OFF"
"-DWITH_ITT=OFF"
"-DWITH_CAROTENE=OFF" ; only visible on arm/aarch64
"-DENABLE_PRECOMPILED_HEADERS=OFF"
"-DOPENCV_GENERATE_PKGCONFIG=ON"
;; CPU-Features:
;; See cmake/OpenCVCompilerOptimizations.cmake
;; (CPU_ALL_OPTIMIZATIONS) for a list of all optimizations
;; BASELINE is the minimum optimization all CPUs must support
;;
;; DISPATCH is the list of optional dispatches.
"-DCPU_BASELINE=SSE2"
;; Build Python bindings.
"-DBUILD_opencv_python3=ON"
,@(match (%current-system)
("x86_64-linux"
'("-DCPU_DISPATCH=NEON;VFPV3;FP16;SSE;SSE2;SSE3;SSSE3;SSE4_1;SSE4_2;POPCNT;AVX;FP16;AVX2;FMA3;AVX_512F;AVX512_SKX"
"-DCPU_DISPATCH_REQUIRE=SSE3,SSSE3,SSE4_1,SSE4_2,AVX,AVX2"))
("armhf-linux"
'("-DCPU_BASELINE_DISABLE=NEON")) ; causes build failures
("aarch64-linux"
'("-DCPU_BASELINE=NEON"
"-DCPU_DISPATCH=NEON;VFPV3;FP16"))
(_ '()))
"-DBUILD_PERF_TESTS=OFF"
"-DBUILD_TESTS=ON"
(string-append "-DOPENCV_EXTRA_MODULES_PATH=" (getcwd)
"/opencv-contrib/modules")
;;Define test data:
(string-append "-DOPENCV_TEST_DATA_PATH=" (getcwd)
"/opencv-extra/testdata")
;; Is ON by default and would try to rebuild 3rd-party protobuf,
;; which we had removed, which would lead to an error:
"-DBUILD_PROTOBUF=OFF"
;; OpenCV tries to use flatbuffers in 3rdparty which we removed
;; so for now we don't buildfor flatbuffer support
;; TODO: make OpenCV use system flatbuffers which involves
;; modifying CMake files
"-DWITH_FLATBUFFERS=OFF"
;; Rebuild protobuf files, because we have a slightly different
;; version than the included one. If we would not update, we
;; would get a compile error later:
"-DPROTOBUF_UPDATE_FILES=ON"
;; For xfeatures2d.
"-DOPENCV_SKIP_FEATURES2D_DOWNLOADING=ON")
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'disable-broken-tests
(lambda _
;; This test fails with "unknown file: Failure"
;; But I couldn't figure out which file was missing:
(substitute* "../opencv-contrib/modules/face/test/test_face_align.cpp"
(("\\bcan_detect_landmarks\\b" all)
(string-append "DISABLED_" all)))
;; This all fails with a comparison between the expected 396 and
;; the actual 440 in file size.
(substitute* "modules/imgcodecs/test/test_exr.impl.hpp"
(("\\breadWrite_32FC1\\b" all)
(string-append "DISABLED_" all)))
;; These fail with protobuf parse errors that come from
;; opencv-extra/alldata.
(substitute* "modules/dnn/test/test_layers.cpp"
(("\\b(Accum|DataAugmentation|Resample|Correlation|Interp)\\b" all)
(string-append "DISABLED_" all)))
;; This test fails on x86-64, loosen the bounds.
;; Expected: (max) < (0.1), actual: 0.2 vs 0.1
(substitute* "modules/photo/test/test_hdr.cpp"
(("0\\.1\\)") "0.222)"))
,@(if (target-aarch64?)
`(;; This test fails on aarch64, loosen the bounds.
;; Expected: (max) < (0.131), actual: 0.207148 vs 0.131
(substitute* "modules/photo/test/test_hdr.cpp"
(("0\\.131") "0.222"))
;; These tests hang forever on aarch64.
(delete-file-recursively "modules/videoio/test/"))
'())
,@(if (target-riscv64?)
`(;; This test fails on riscv64, loosen the bounds.
;; Expected: (max) < (0.1), actual: 0.220829 vs 0.1
(substitute* "modules/photo/test/test_hdr.cpp"
(("0\\.1") "0.240"))
;; Expected equality of these values:
;; ellipses.size()
;; Which is: 668
;; ellipses_size
;; Which is: 2449
(substitute* "../opencv-contrib/modules/ximgproc/test/test_fld.cpp"
(("\\bManySmallCircles\\b" all)
(string-append "DISABLED_" all))))
'())))
(add-after 'unpack 'unpack-submodule-sources
(lambda* (#:key inputs #:allow-other-keys)
(mkdir "../opencv-extra")
(mkdir "../opencv-contrib")
(copy-recursively (assoc-ref inputs "opencv-extra")
"../opencv-extra")
(copy-recursively (assoc-ref inputs "opencv-contrib")
"../opencv-contrib")
;; Disable downloads of Boost and VGG descriptors as we include
;; them in native inputs.
(substitute* "../opencv-contrib/modules/xfeatures2d/CMakeLists.txt"
(("download_(boost|vgg)_descriptors") "#"))
(copy-recursively (assoc-ref inputs "opencv-3rdparty-boost")
"../downloads/xfeatures2d")
(for-each make-file-writable
(find-files "../downloads/xfeatures2d" "."))
(copy-recursively (assoc-ref inputs "opencv-3rdparty-vgg")
"../downloads/xfeatures2d")))
(add-after 'build 'do-not-install-3rdparty-file
(lambda _
(substitute* "cmake_install.cmake"
(("file\\(INSTALL .*3rdparty/include/opencl/LICENSE.txt.*")
""))))
(add-before 'check 'start-xserver
(lambda* (#:key inputs #:allow-other-keys)
(let ((xorg-server (assoc-ref inputs "xorg-server"))
(disp ":1"))
(setenv "HOME" (getcwd))
(setenv "DISPLAY" disp)
;; There must be a running X server and make check doesn't start one.
;; Therefore we must do it.
(zero? (system (format #f "~a/bin/Xvfb ~a &" xorg-server disp)))))))))
(native-inputs
`(("pkg-config" ,pkg-config)
("xorg-server" ,xorg-server-for-tests) ;For running the tests
;; These are files that are derived from the binary descriptors that
;; are part of the BinBoost package. The BinBoost package is released
;; under GPLv2+. See
;; https://www.epfl.ch/labs/cvlab/research/descriptors-and-keypoints/research-detect-binboost/
;; See xfeatures2d/cmake/download_boostdesc.cmake for commit hash.
("opencv-3rdparty-boost"
,(let ((commit "34e4206aef44d50e6bbcd0ab06354b52e7466d26"))
(origin
(method git-fetch)
(uri (git-reference (url "https://github.com/opencv/opencv_3rdparty")
(commit commit)))
(file-name (git-file-name "opencv_3rdparty" commit))
(sha256
(base32
"13yig1xhvgghvxspxmdidss5lqiikpjr0ddm83jsi0k85j92sn62")))))
;; These are the Visual Geometry Group descriptors, released under
;; BSD-3. They are generated files produced by the DLCO framework.
;; See xfeatures2d/cmake/download_vgg.cmake for commit hash.
("opencv-3rdparty-vgg"
,(let ((commit "fccf7cd6a4b12079f73bbfb21745f9babcd4eb1d"))
(origin
(method git-fetch)
(uri (git-reference (url "https://github.com/opencv/opencv_3rdparty")
(commit commit)))
(file-name (git-file-name "opencv_3rdparty" commit))
(sha256
(base32
"0r9fam8dplyqqsd3qgpnnfgf9l7lj44di19rxwbm8mxiw0rlcdvy")))))
("opencv-extra"
,(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/opencv/opencv_extra")
(commit version)))
(file-name (git-file-name "opencv_extra" version))
(sha256
(base32
"16gykga4cc8q8iqx9sj25ggxrp6mqbppwwib734nhlk1b6s2q15j"))))
("opencv-contrib"
,(origin
(method git-fetch)
(uri (git-reference (url "https://github.com/opencv/opencv_contrib")
(commit version)))
(file-name (git-file-name "opencv_contrib" version))
(sha256
(base32
"07sanb0kb90rwghlp4jpgvmicr39hgrsjmsc5nifcryw3d0r0m14"))))))
(inputs
(list eigen
ffmpeg-4
;; TODO: add gstreamer
gtk+
gtkglext
hdf5
ilmbase
imath ;should be propagated by openexr
jasper
libgphoto2
libjpeg-turbo
libpng
libtiff
libwebp
openblas
opencl-headers
openexr
openmpi
openjpeg
protobuf
python
python-numpy
vtk
zlib))
;; These three CVEs are not a problem of OpenCV, see:
;; https://github.com/opencv/opencv/issues/10998
(properties '((lint-hidden-cve . ("CVE-2018-7712"
"CVE-2018-7713"
"CVE-2018-7714"))))
(synopsis "Computer vision library")
(description "OpenCV is a library aimed at real-time computer vision,
including several hundred computer vision algorithms. It can be used to do
things like:
@itemize
@item image and video input and output
@item image and video processing
@item displaying
@item feature recognition
@item segmentation
@item facial recognition
@item stereo vision
@item structure from motion
@item augmented reality
@item machine learning
@end itemize\n
This package includes the Python bindings for OpenCV, which are also known as
the OpenCV-Python library.")
(home-page "https://opencv.org/")
(license license:bsd-3)))
(define-public vips
(package
(name "vips")
(version "8.13.1")
(source
(origin
(method url-fetch)
(uri (string-append
"https://github.com/libvips/libvips/releases/download/v"
version "/vips-" version ".tar.gz"))
(sha256
(base32 "00kp3439jcqv9l2gcjg88xzvlq8clv54z1m3x66i3chvarz7ndxd"))))
(build-system gnu-build-system)
(native-inputs
(list gobject-introspection pkg-config))
(inputs
(list expat
fftw
giflib
glib
hdf5
imagemagick
lcms
libexif
libgsf
libjpeg-turbo
libpng
(librsvg-for-system)
libtiff
libxml2
libwebp
matio
niftilib
openexr-2
orc
pango
poppler))
(home-page "https://libvips.github.io/libvips/")
(synopsis "Multithreaded image processing system with low memory needs")
(description
"VIPS is a demand-driven, horizontally threaded image processing library.
It's particularly good at processing large images, working with colour,
scientific analysis, and general research & development.
Compared to most image processing libraries VIPS needs little RAM and runs
quickly, especially on machines with more than one CPU core. This is primarily
due to its architecture which automatically parallelises the image workflows.")
(license license:lgpl2.1+)))
(define-public gmic
(package
(name "gmic")
(version "3.4.1")
(source
(origin
(method url-fetch)
(uri (string-append "https://gmic.eu/files/source/gmic_"
version ".tar.gz"))
(sha256
(base32 "0kyr91y35l2fn4f7hx17n5j8pl63kw6ik9ap09pa2n9bdsbzrjcp"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #f ;there are no tests
#:configure-flags '("-DBUILD_LIB_STATIC=OFF"
"-DENABLE_DYNAMIC_LINKING=ON"
"-DENABLE_LTO=ON")
#:phases
(modify-phases %standard-phases
(add-before 'configure 'set-LDFLAGS
(lambda* (#:key inputs outputs #:allow-other-keys)
(setenv "LDFLAGS"
(string-append
"-Wl,-rpath="
(assoc-ref outputs "out") "/lib")))))))
(native-inputs
(list pkg-config))
(inputs
(list curl
fftw
graphicsmagick
imath
libjpeg-turbo
libpng
libtiff
libx11
openexr
zlib))
(home-page "https://gmic.eu/")
(synopsis "Full-featured framework for digital image processing")
(description "G'MIC is a full-featured framework for digital image
processing. It provides several user interfaces to convert / manipulate
/ filter / visualize generic image datasets, ranging from 1D scalar
signals to 3D+t sequences of multi-spectral volumetric images, hence
including 2D color images.")
;; Dual-licensed, either license applies.
(license (list license:cecill license:cecill-c))))
(define-public gmic-qt
(package
(inherit gmic)
(name "gmic-qt")
(arguments
(substitute-keyword-arguments (package-arguments gmic)
((#:configure-flags _)
`(list "-DGMIC_QT_HOST=none" "-DENABLE_DYNAMIC_LINKING=ON"
(string-append "-DGMIC_LIB_PATH="
(assoc-ref %build-inputs "gmic") "/lib")))
((#:phases phases)
`(modify-phases ,phases
(add-after 'unpack 'qt-chdir
(lambda _ (chdir "gmic-qt") #t))))))
(native-inputs
(list pkg-config qttools-5))
(inputs
(modify-inputs (package-inputs gmic)
(prepend gmic qtbase-5)))
(synopsis "Qt frontend for the G'MIC image processing framework")
(license license:gpl3+)))
(define-public gmic-qt-gimp
(package
(inherit gmic-qt)
(name "gmic-qt-gimp")
(inputs
;; GIMP and its dependencies.
(modify-inputs (package-inputs gmic-qt)
(prepend gimp gdk-pixbuf cairo gegl)))
(arguments
(substitute-keyword-arguments (package-arguments gmic-qt)
((#:configure-flags flags)
'(list "-DGMIC_QT_HOST=gimp" "-DENABLE_DYNAMIC_LINKING=ON"
(string-append "-DGMIC_LIB_PATH="
(assoc-ref %build-inputs "gmic") "/lib")))))
(synopsis "GIMP plugin for the G'MIC image processing framework")))
(define-public nip2
(package
(name "nip2")
(version "8.7.1")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/libvips/nip2/releases/download/v"
version "/nip2-" version ".tar.gz" ))
(sha256
(base32 "0l7n427njif53npqn02gfjjly8y3khbrkzqxp10j5vp9h97psgiw"))))
(build-system gnu-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
;; test_conv.ws keep failing so disabling for now.
(add-after 'unpack 'disable-test-conv
(lambda _
(delete-file "test/workspaces/test_conv.ws")
#t))
(add-before 'check 'set-home
(lambda _
(setenv "HOME" "/tmp") #t)))))
(inputs
(list vips
glib
libtiff
gtk+-2
libxml2
libexif
libjpeg-turbo ;required by vips.pc
(librsvg-for-system)
fftw
libgsf
imagemagick
orc
matio
lcms
libwebp
openexr-2
poppler
gsl))
(native-inputs
(list flex bison pkg-config))
(home-page "https://github.com/libvips/nip2")
(synopsis "Spreadsheet-like GUI for libvips")
(description "This package provide a graphical user interface (GUI) for
the VIPS image processing library. It's a little like a spreadsheet: you
create a set of formula connecting your objects together, and on a change nip2
recalculates.")
(license license:gpl2+)))
(define-public paraview
(package
(name "paraview")
(version "5.11.1")
(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 "0m1lgkl95f0pyhxp97gq2rf8hibv39v4c49imfj1va40z0flvard"))
(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"
"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
nlohmann-json ;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")
(version "3.5.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/vxl/vxl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0iqq4lm51l5gvkax6r79ypifqmgir3p3vman9gsc2085d2agjvbs"))
(modules '((guix build utils)))
;; TODO: vxl includes an old version of dcmtk. It won't build with
;; version 3.6.x.
(snippet
'(begin
(for-each delete-file-recursively
'("v3p/bzlib/"
"v3p/geotiff/"
"v3p/jpeg/"
"v3p/png/"
"v3p/tiff/"
"v3p/zlib/"))
(substitute* "v3p/CMakeLists.txt"
(("add_subdirectory\\((tiff|png|jpeg|zlib|bzlib|geotiff)\\)")
""))
#t))))
(build-system cmake-build-system)
(inputs
(list libgeotiff libtiff libjpeg-turbo libpng zlib))
(home-page "https://github.com/vxl/vxl/")
(synopsis "Collection of C++ libraries for computer vision")
(description "VXL (the Vision-something-Libraries) is a collection of C++
libraries designed for computer vision research and implementation.")
(license license:bsd-3)))
(define-public vxl-1
(package (inherit vxl)
(name "vxl")
(version "1.18.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/vxl/vxl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1g4mr2cc58jwm0vasscbd4y5380wj3ahkvq121z4gs83fhavvxgz"))
(modules '((guix build utils)))
(snippet
'(begin
(for-each delete-file-recursively
'("v3p/bzlib/"
"v3p/geotiff/"
"v3p/png/"
"v3p/tiff/"
"v3p/zlib/"))
(substitute* "v3p/CMakeLists.txt"
(("add_subdirectory\\((tiff|png|jpeg|zlib|bzlib|geotiff)\\)")
""))
#t))))
(arguments
`(#:configure-flags
;; Needed for itk-snap
(list "-DVNL_CONFIG_LEGACY_METHODS=ON")))))
(define-public insight-toolkit
(package
(name "insight-toolkit")
(version "5.0.0")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/InsightSoftwareConsortium/ITK/"
"releases/download/v" version "/InsightToolkit-"
version ".tar.xz"))
(sha256
(base32 "0bs63mk4q8jmx38f031jy5w5n9yy5ng9x8ijwinvjyvas8cichqi"))))
(build-system cmake-build-system)
(outputs '("out" "python"))
(arguments
(list #:tests? #f ; tests require network access and external data
#:configure-flags
#~(list "-DITK_USE_GPU=ON"
"-DITK_USE_SYSTEM_LIBRARIES=ON"
"-DITK_USE_SYSTEM_GOOGLETEST=ON"
"-DITK_USE_SYSTEM_CASTXML=ON"
"-DITK_BUILD_SHARED=ON"
"-DITK_WRAPPING=ON"
"-DITK_WRAP_PYTHON=ON"
"-DITK_DYNAMIC_LOADING=ON"
(let* ((python-version
#$(version-major+minor
(package-version (this-package-input "python"))))
(python-lib-path
(string-append #$output:python
"/lib/python" python-version
"/site-packages")))
(string-append "-DPY_SITE_PACKAGES_PATH=" python-lib-path))
;; This prevents "GTest::GTest" from being added to the ITK_LIBRARIES
;; variable in the installed CMake files. This is necessary as other
;; packages using insight-toolkit could not be configured otherwise.
"-DGTEST_ROOT=gtest"
"-DCMAKE_CXX_STANDARD=17")
#:phases #~(modify-phases %standard-phases
(add-after 'unpack 'do-not-tune
(lambda _
(substitute* "CMake/ITKSetStandardCompilerFlags.cmake"
(("-mtune=native")
""))))
(add-after 'unpack 'ignore-warnings
(lambda _
(substitute* "Wrapping/Generators/Python/CMakeLists.txt"
(("-Werror") "")))))))
(inputs
(list eigen
expat
fftw
fftwf
hdf5
libjpeg-turbo
libpng
libtiff
mesa-opencl
perl
python
tbb
vxl-1
zlib))
(native-inputs
(list castxml googletest pkg-config swig which))
;; The 'CMake/ITKSetStandardCompilerFlags.cmake' file normally sets
;; '-mtune=native -march=corei7', suggesting there's something to be
;; gained from CPU-specific optimizations.
(properties '((tunable? . #t)))
(home-page "https://github.com/InsightSoftwareConsortium/ITK/")
(synopsis "Scientific image processing, segmentation and registration")
(description "The Insight Toolkit (ITK) is a toolkit for N-dimensional
scientific image processing, segmentation, and registration. Segmentation is
the process of identifying and classifying data found in a digitally sampled
representation. Typically the sampled representation is an image acquired
from such medical instrumentation as CT or MRI scanners. Registration is the
task of aligning or developing correspondences between data. For example, in
the medical environment, a CT scan may be aligned with a MRI scan in order to
combine the information contained in both.")
(license license:asl2.0)))
(define-public insight-toolkit-4
(package (inherit insight-toolkit)
(version "4.13.2")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/InsightSoftwareConsortium/ITK/"
"releases/download/v" version "/InsightToolkit-"
version ".tar.xz"))
(sha256
(base32 "19cgfpd63gqrvc3m27m394gy2d7w79g5y6lvznb5qqr49lihbgns"))))
(outputs '("out"))
(arguments
(list #:tests? #f ; tests require network access and external data
#:configure-flags #~'("-DITKV3_COMPATIBILITY=ON" ; needed for itk-snap
"-DITK_USE_GPU=ON"
"-DITK_USE_SYSTEM_LIBRARIES=ON"
"-DITK_USE_SYSTEM_GOOGLETEST=ON"
"-DITK_USE_SYSTEM_VXL=ON")))
(native-inputs
(list googletest pkg-config))))
(define-public insight-toolkit-4.12
(package (inherit insight-toolkit-4)
(version "4.12.2")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/itk/itk/4.12/"
"InsightToolkit-" version ".tar.xz"))
(sha256
(base32 "1qw9mxbh083siljygahl4gdfv91xvfd8hfl7ghwii19f60xrvn2w"))))
(arguments
(substitute-keyword-arguments (package-arguments insight-toolkit-4)
((#:configure-flags cf #~'())
;; error: ISO C++17 does not allow dynamic exception specifications
#~(cons* "-DCMAKE_CXX_FLAGS=-std=c++14" #$cf))))))
(define-public itk-snap
(package
(name "itk-snap")
(version "3.8.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://git.code.sf.net/p/itk-snap/src")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "15i5ixpryfrbf3vrrb5rici8fb585f25k0v1ljds16bp1f1msr4q"))
(patches (search-patches "itk-snap-alt-glibc-compat.patch"))))
(build-system cmake-build-system)
(arguments
`(#:configure-flags
(list "-DSNAP_VERSION_GIT_SHA1=release"
"-DSNAP_VERSION_GIT_BRANCH=release"
"-DSNAP_VERSION_GIT_TIMESTAMP=0"
"-DSNAP_PACKAGE_QT_PLUGINS=OFF"
"-DCMAKE_POSITION_INDEPENDENT_CODE=ON")
#:phases
(modify-phases %standard-phases
;; During the installation phase all libraries provided by all
;; dependencies will be copied to the lib directory. That's insane,
;; so we disable this.
(add-after 'unpack 'do-not-copy-dependencies
(lambda _
(substitute* "CMakeLists.txt"
(("install_qt5_executable\
\\(\\$\\{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-5"))))))))))
(inputs
(list bash-minimal
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-5
vxl-1
zlib))
(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")))))))
(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+)))
(define-public metapixel
;; Follow stable branch.
(let ((commit "98ee9daa093b6c334941242e63f90b1c2876eb4f"))
(package
(name "metapixel")
(version (git-version "1.0.2" "1" commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/schani/metapixel")
(commit commit)
;; TODO: Package rwimg and lispreader?
(recursive? #t)))
(file-name (git-file-name name version))
(sha256
(base32 "0r7n3a6bvcxkbpda4mwmrpicii09iql5z69nkjqygkwxw7ny3309"))))
(build-system gnu-build-system)
(arguments
(list
#:tests? #f ; No tests.
#:make-flags
#~(list
(string-append "PREFIX=" #$output)
(format #f "MANPAGE_XSL=~a/xml/xsl/~a-~a/manpages/docbook.xsl"
#$(this-package-native-input "docbook-xsl")
#$(package-name
(this-package-native-input "docbook-xsl"))
#$(package-version
(this-package-native-input "docbook-xsl"))))
#:phases
#~(modify-phases %standard-phases
(delete 'configure)
(add-before 'install 'fix-directory-creation
(lambda _
(mkdir-p (string-append #$output "/share/man/man1")))))))
(inputs
(list giflib libjpeg-turbo libpng
perl))
(native-inputs
(list docbook-xml-4.2 docbook-xsl
libxslt pkg-config))
(home-page "https://www.complang.tuwien.ac.at/schani/metapixel/")
(synopsis "Photomosaics generator")
(description "Metapixel is a program for generating photomosaics. It can
generate classical photomosaics, in which the source image is viewed as a
matrix of equally sized rectangles for each of which a matching image is
substituted, as well as collage-style photomosaics, in which rectangular parts
of the source image at arbitrary positions (i.e. not aligned to a matrix) are
substituted by matching images.")
(license license:gpl2))))
(define-public scantailor-advanced
(let ((commit "3d1e74e6ace413733511086934a66f4e3f7a6027"))
(package
(name "scantailor-advanced")
(version (string-append "1.0.16-" (string-take commit 7)))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/4lex4/scantailor-advanced")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"0kixwjb2x457dq7927hkh34c803p7yh1pmn6n61rk9shqrcg492h"))))
(build-system qt-build-system)
(native-inputs
(list qttools-5))
(inputs
`(("boost" ,boost)
("libjpeg" ,libjpeg-turbo)
("libpng" ,libpng)
("libtiff" ,libtiff)
("qtbase" ,qtbase-5)
("qtsvg-5" ,qtsvg-5)
("zlib" ,zlib)))
(arguments
`(#:phases
(modify-phases %standard-phases
;; Some tests require a display and fail with offscreen mode.
(add-after 'unpack 'disable-failing-tests
(lambda _
(setenv "ARGS" "--exclude-regex \"imageproc_.*\"")
#t)))))
(home-page "https://github.com/4lex4/scantailor-advanced")
(synopsis "Clean up scanned pages")
(description "Scan Tailor is an interactive post-processing tool for
scanned pages. It performs operations such as page splitting, deskewing,
adding/removing borders, and others. You give it raw scans, and you get pages
ready to be printed or assembled into a PDF or DJVU file. Scanning, optical
character recognition, and assembling multi-page documents are out of scope of
this project.
Scan Tailer Advanced is a fork of Scan Tailer that merges Scan Tailor Featured
and Scan Tailor Enhanced versions as well as including many more bug fixes.")
(license license:gpl3+))))
(define-public stiff
(package
(name "stiff")
(version "2.4.0")
(source
(origin
(method url-fetch)
(uri (string-append "https://www.astromatic.net/download/stiff/stiff-"
version ".tar.gz"))
(sha256
(base32 "14m92dskzw7bwsr64ha4p0mj3ndv13gwcbfic3qxrs3zq5353s7l"))))
(build-system gnu-build-system)
(inputs
(list libtiff zlib libjpeg-turbo))
(home-page "https://www.astromatic.net/software/stiff")
(synopsis "Convert scientific FITS images to TIFF format")
(description
"STIFF is a program that converts scientific @acronym{FITS, Flexible Image
Transport System} images to the more popular TIFF format for illustration
purposes.")
(license license:gpl3+)))
(define-public python-imgviz
(package
(name "python-imgviz")
(version "1.2.6")
(source
(origin
;; PyPi tarball lacks tests.
(method git-fetch)
(uri (git-reference
(url "https://github.com/wkentaro/imgviz.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1bm0wdv5p26i8nl4kx3145cz553v401sgbpgc96sddzjfmfiydcw"))
(snippet
#~(begin (use-modules (guix build utils))
(substitute* "imgviz/draw.py"
(("collections\\.Iterable") "collections.abc.Iterable"))
(substitute* "imgviz/tile.py"
(("collections\\.Sequence") "collections.abc.Sequence"))))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(replace 'check
(lambda* (#:key inputs outputs tests? #:allow-other-keys)
(when tests?
(add-installed-pythonpath inputs outputs)
(invoke "pytest" "-v" "tests"))
#t)))))
(propagated-inputs
(list python-matplotlib python-numpy python-pillow python-pyyaml))
(native-inputs (list python-pytest))
(home-page "http://github.com/wkentaro/imgviz")
(synopsis "Image Visualization Tools")
(description "Python library for object detection, semantic and instance
segmentation.")
(license license:expat)))
(define-public python-pims
(package
(name "python-pims")
(version "0.6.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "PIMS" version))
(sha256
(base32 "0fsg353mbbj1ad06nwrp8p9xcrzy6rca6b52nvlbraaf3m309dz2"))))
(build-system pyproject-build-system)
(arguments
(list
#:test-flags
;; We don't have all the (sometimes very large) data files, so we skip
;; these tests.
'(list "--ignore=pims/tests/test_imseq.py"
"--ignore=pims/tests/test_norpix.py"
"-k"
(string-append " not TestImageReaderTIFF"
" and not TestOpenFiles"
" and not TestSpeStack"
" and not TestTiffStack_pil"
" and not TestTiffStack_tifffile"
" and not TestVideo_ImageIO"))))
(propagated-inputs
(list python-imageio python-numpy python-slicerator))
(native-inputs (list python-pytest))
(home-page "https://github.com/soft-matter/pims")
(synopsis "Python Image Sequence")
(description "Scientific video can be packaged in various ways: familiar
video formats like @file{.AVI} and @file{.MOV}, folders full of numbered
images, or \"stacks\" of TIFF images. Each of these requires a separate
Python module. And, once loaded, they have different methods for accessing
individual images, looping through the images in bulk, accessing a specific
range, or dealing with multidimensional files. PIMS can do all of these using
a consistent interface, handling the differences between different inputs
invisibly.")
(license license:bsd-3)))
(define-public python-spatial-image
(package
(name "python-spatial-image")
(version "1.0.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "spatial_image" version))
(sha256
(base32 "0blyjwgv6bqpg7r3f4dcs7x27ysfm8n9y0zk5j7dxj74lma3wdsm"))))
(build-system pyproject-build-system)
(propagated-inputs (list python-numpy python-pytest python-pytest-mypy
python-xarray python-xarray-dataclasses))
(native-inputs (list python-flit-core python-pytest))
(home-page "https://github.com/spatial-image/spatial-image")
(synopsis "Multi-dimensional spatial image data structure")
(description "This package implements a multi-dimensional spatial image
data structure for scientific Python.
To facilitate:
@itemize
@item Multi-scale processing and analysis
@item Registration
@item Resampling
@item Subregion parallel processing
@item Coupling with meshes, point sets, and annotations
@end itemize
with scientific images, which are typically multi-dimensional with anisotropic
sampling, this package provides a spatial-image data structure. In addition
to an N-dimensional array of pixel values, spatial metadata defines the
location of the pixel sampling grid in space time. It also labels the array
dimensions. This metadata is easily utilized and carried through image
processing pipelines.")
(license license:expat)))
(define-public labelme
(package
(name "labelme")
(version "4.5.13")
(source
(origin
;; PyPi tarball lacks tests.
(method git-fetch)
(uri (git-reference
(url "https://github.com/wkentaro/labelme.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0cmi2xb4dgh7738l259rgwhn9l134f0vnaaqc2gflc5yr3lqhrv2"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'loosen-requirements
(lambda _
;; Don't require an outdated version of matplotlib.
(substitute* "setup.py"
(("matplotlib<3\\.3")
"matplotlib"))))
(add-before 'check 'start-xserver
(lambda* (#:key inputs #:allow-other-keys)
(let ((xorg-server (assoc-ref inputs "xorg-server")))
;; Options taken from CI workflow.
(system (string-append xorg-server "/bin/Xvfb :99 -screen 0 "
"1920x1200x24 -ac +extension GLX +render "
"-noreset &"))
(setenv "DISPLAY" ":99.0"))))
(replace 'check
(lambda* (#:key inputs outputs tests? #:allow-other-keys)
(when tests?
(add-installed-pythonpath inputs outputs)
;; Fails when invoking help2man for unknown reason.
(delete-file "tests/docs_tests/man_tests/test_labelme_1.py")
;; One test hangs.
(delete-file "tests/labelme_tests/widgets_tests/test_label_dialog.py")
;; Calls incompatible function signatures.
(delete-file "tests/labelme_tests/widgets_tests/test_label_list_widget.py")
(setenv "MPLBACKEND" "agg")
(invoke "pytest" "-v" "tests" "-m" "not gpu")))))))
(propagated-inputs
(list python-imgviz
python-matplotlib
python-numpy
python-pillow
python-pyyaml
python-qtpy
python-termcolor))
(native-inputs
(list python-pytest python-pytest-qt xorg-server-for-tests))
(home-page "https://github.com/wkentaro/labelme")
(synopsis
"Image Polygonal Annotation")
(description
"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)))
(define-public libansilove
(package
(name "libansilove")
(version "1.4.1")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ansilove/libansilove")
(commit (string-append version))))
(file-name (git-file-name name version))
(sha256
(base32
"169njlck4a2bmf1kmjas1w594hyda543ykdnwg7fwkviij39l9z6"))))
(build-system cmake-build-system)
(arguments
(list #:tests? #f)) ; No tests included
(native-inputs
(list gd))
(home-page "https://www.ansilove.org/")
(synopsis "Library for converting ANSI, ASCII, and other formats to PNG")
(description
"libansilove is a library for converting artscene file types to PNG images,
including ANSI (.ANS) and many others. The library primarily serves to support
the ansilove tool.")
(license license:bsd-2)))
(define-public ansilove
(package
(name "ansilove")
(version "4.2.0")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ansilove/ansilove")
(commit (string-append version))))
(file-name (git-file-name name version))
(sha256
(base32
"1h9r759krjl8wi68yxs1d46qfrx6v89a8vmmv3aqym8vn9x430kh"))))
(build-system cmake-build-system)
(native-inputs
(list libansilove))
(home-page "https://www.ansilove.org/")
(synopsis "ANSI and ASCII art to PNG converter")
(description
"AnsiLove is an ANSI and ASCII art to PNG converter, allowing to convert
ANSI and artscene-related file formats into PNG images, supporting ANSI (.ANS),
PCBoard (.PCB), Binary (.BIN), Artworx (.ADF), iCE Draw (.IDF), Tundra (.TND)
and XBin (.XB) formats.")
(license license:bsd-2)))
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