54ef40a1f7
* gnu/packages/patches/mia-fix-boost-headers.patch: New patch. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/image-processing.scm (mia): Update to 2.4.7. [source]: Apply patch. [configure-flags]: Use the more conventional OFF option value (instead of 0). [inputs]: Use new style. Replace python2-lxml by python-lxml. Replace vtk by vtk-7. [native-inputs]: Use new style. Replace python-2 with python-wrapper.
1365 lines
53 KiB
Scheme
1365 lines
53 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
|
||
;;; Copyright © 2017 John Darrington <jmd@gnu.org>
|
||
;;; Copyright © 2017, 2019, 2022 Ricardo Wurmus <rekado@elephly.net>
|
||
;;; Copyright © 2014, 2021-2022 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 Efraim Flashner <efraim@flashner.co.il>
|
||
;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
|
||
;;; Copyright © 2020, 2021 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 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>
|
||
;;;
|
||
;;; 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 (gnu packages)
|
||
#:use-module (gnu packages algebra)
|
||
#:use-module (gnu packages bison)
|
||
#:use-module (gnu packages boost)
|
||
#:use-module (gnu packages check)
|
||
#:use-module (gnu packages compression)
|
||
#: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 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 pdf)
|
||
#:use-module (gnu packages perl)
|
||
#:use-module (gnu packages photo)
|
||
#:use-module (gnu packages pkg-config)
|
||
#:use-module (gnu packages protobuf)
|
||
#:use-module (gnu packages python)
|
||
#:use-module (gnu packages python-check)
|
||
#:use-module (gnu packages python-xyz)
|
||
#:use-module (gnu packages qt)
|
||
#:use-module (gnu packages serialization)
|
||
#:use-module (gnu packages sqlite)
|
||
#:use-module (gnu packages tbb)
|
||
#: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 "0.7.00")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/mrirecon/bart")
|
||
(commit "d1b0e576c3f759089915565d5bf57832acf7b03e")))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "159rj3agr9pb9lg38b56rnw3d8wcbkmb2n718z26zpy4c6a6d9rn"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
(list
|
||
#:test-target "utest"
|
||
#:make-flags #~(list
|
||
(string-append "PREFIX=" #$output)
|
||
"OPENBLAS=1"
|
||
"SCALAPACK=1"
|
||
(string-append "BLAS_BASE=" #$(this-package-input "openblas"))
|
||
(string-append "FFTW_BASE=" #$(this-package-input "fftw")))
|
||
#: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 "3.6.7")
|
||
(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 "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
|
||
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"))))
|
||
(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
|
||
;; 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
|
||
(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,
|
||
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 "1.1.1")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/AcademySoftwareFoundation/OpenColorIO")
|
||
(commit (string-append "v" version))))
|
||
(sha256
|
||
(base32 "12srvxca51czpfjl0gabpidj9n84mw78ivxy5w75qhq2mmc798sb"))
|
||
(file-name (git-file-name name version))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
`(begin
|
||
;; Remove bundled tarballs, patches, and .jars(!). XXX: Upstream
|
||
;; claims to have fixed USE_EXTERNAL_YAML, but it still fails with:
|
||
;; https://github.com/AcademySoftwareFoundation/OpenColorIO/issues/517
|
||
;; When removing it, also remove it from the licence field comment.
|
||
(for-each delete-file-recursively
|
||
(filter
|
||
(lambda (full-name)
|
||
(let ((file (basename full-name)))
|
||
(not (or (string-prefix? "yaml-cpp-0.3" file)
|
||
(string=? "unittest.h" file)))))
|
||
(find-files "ext" ".*")))
|
||
|
||
#t))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:configure-flags
|
||
(list (string-append "-DCMAKE_CXX_FLAGS="
|
||
"-Wno-error=deprecated-declarations "
|
||
"-Wno-error=unused-function")
|
||
"-DOCIO_BUILD_STATIC=OFF"
|
||
;; "-DUSE_EXTERNAL_YAML=ON"
|
||
"-DUSE_EXTERNAL_TINYXML=ON"
|
||
"-DUSE_EXTERNAL_LCMS=ON")
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'patch-test-suite
|
||
(lambda _
|
||
(substitute* "src/core_tests/CMakeLists.txt"
|
||
(("/bin/sh") (which "bash")))
|
||
#t)))))
|
||
(native-inputs
|
||
(list git pkg-config))
|
||
(inputs
|
||
;; XXX Adding freeglut, glew, ilmbase, mesa, and openimageio for
|
||
;; ocioconvert fails: error: conflicting declaration ?typedef void
|
||
;; (* PFNGLGETFRAGMENTMATERIALFVSGIXPROC)(GLenum, GLenum, GLfloat*)
|
||
(list lcms openexr-2 tinyxml))
|
||
(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 (list license:expat ; docs/ociotheme/static, ext/yaml-cpp-*
|
||
license:zlib ; src/core/md5
|
||
license:bsd-3)))) ; the rest
|
||
|
||
(define-public vtk
|
||
(package
|
||
(name "vtk")
|
||
(version "9.0.1")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://vtk.org/files/release/"
|
||
(version-major+minor version)
|
||
"/VTK-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1ir2lq9i45ls374lcmjzw0nrm5l5hnm1w47lg8g8d0n2j7hsaf8v"))
|
||
(patches
|
||
(search-patches "vtk-fix-freetypetools-build-failure.patch"))
|
||
(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" "libproj" "libxml2" "lz4"
|
||
"netcdf" "ogg" "png" "sqlite" "theora" "tiff" "zlib"))
|
||
#t))))
|
||
(properties `((release-monitoring-url . "https://vtk.org/download/")))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
'(#: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_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_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
|
||
eigen
|
||
expat
|
||
freetype
|
||
gl2ps
|
||
glew
|
||
glu
|
||
hdf5
|
||
libjpeg-turbo
|
||
jsoncpp
|
||
libtheora
|
||
libx11
|
||
libxml2
|
||
libxt
|
||
lz4
|
||
mesa
|
||
netcdf
|
||
libpng
|
||
proj
|
||
python
|
||
;("pugixml" ,pugixml)
|
||
sqlite
|
||
libtiff
|
||
xorgproto
|
||
zlib))
|
||
(propagated-inputs
|
||
;; VTK's 'VTK-vtk-module-find-packages.cmake' calls
|
||
;; 'find_package(THEORA)', which in turns looks for libogg.
|
||
(list libogg))
|
||
(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"))))
|
||
(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
|
||
(name "opencv")
|
||
(version "4.5.4")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/opencv/opencv")
|
||
(commit version)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0gf2xs3r4s51m20mpf0wdidpk0xzp3m2w6jx72fwldhn0pshlmcj"))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
'(begin
|
||
;; Remove external libraries. We have almost all available
|
||
;; in Guix:
|
||
(with-directory-excursion "3rdparty"
|
||
(for-each delete-file-recursively
|
||
'("carotene"
|
||
"cpufeatures"
|
||
"ffmpeg"
|
||
"include"
|
||
"ippicv"
|
||
"ittnotify"
|
||
"libjasper"
|
||
"libjpeg"
|
||
"libjpeg-turbo"
|
||
"libpng"
|
||
"libtengine"
|
||
"libtiff"
|
||
"libwebp"
|
||
"openexr"
|
||
"openjpeg"
|
||
"openvx"
|
||
"protobuf"
|
||
;;"quirc"
|
||
"tbb"
|
||
"zlib")))
|
||
|
||
;; Milky icon set is non-free:
|
||
(delete-file-recursively "modules/highgui/src/files_Qt/Milky")
|
||
|
||
;; Some jars found:
|
||
(for-each delete-file
|
||
'("modules/java/test/pure_test/lib/junit-4.11.jar"
|
||
"samples/java/sbt/sbt/sbt-launch.jar"))))))
|
||
(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"
|
||
|
||
,@(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"
|
||
|
||
;; 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"
|
||
|
||
;; xfeatures2d disabled, because it downloads extra binaries from
|
||
;; https://github.com/opencv/opencv_3rdparty
|
||
;; defined in xfeatures2d/cmake/download_{vgg|bootdesc}.cmake
|
||
;; Cmp this bug entry:
|
||
;; https://github.com/opencv/opencv_contrib/issues/1131
|
||
"-DBUILD_opencv_xfeatures2d=OFF")
|
||
#: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"
|
||
(("(TEST\\(CV_Face_FacemarkKazemi, )(can_detect_landmarks\\).*)"
|
||
all pre post)
|
||
(string-append pre "DISABLED_" post)))
|
||
|
||
;; This test fails with a comparison between the expected 396 and
|
||
;; the actual 440 in file size.
|
||
(substitute* "modules/imgcodecs/test/test_exr.impl.hpp"
|
||
(("(TEST\\(Imgcodecs_EXR, )(readWrite_32FC1\\).*)" all pre post)
|
||
(string-append pre "DISABLED_" post)))
|
||
|
||
;; These fail with protobuf parse errors that come from
|
||
;; opencv-extra/testdata.
|
||
(substitute* "modules/dnn/test/test_layers.cpp"
|
||
(("(TEST_P\\(Test_Caffe_layers, )\
|
||
(Accum\\).*|DataAugmentation\\).*|Resample\\).*|Correlation\\).*)" all pre post)
|
||
(string-append pre "DISABLED_" post)))))
|
||
(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")))
|
||
(add-after 'build 'do-not-install-3rdparty-file
|
||
(lambda _
|
||
(substitute* "cmake_install.cmake"
|
||
(("file\\(INSTALL .*source/3rdparty/include/opencl/LICENSE.txt.*") "\n"))))
|
||
(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
|
||
("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 "1fg2hxdvphdvagc2fkmhqk7qql9mp7pj2bmp8kmd7vicpr72qk82"))))
|
||
("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 "0ga0l4ranp1834gxgp487ll1amvmssa02l2nk5ja5w0rx4d8hh26"))))))
|
||
(inputs
|
||
(list ffmpeg
|
||
gtk+
|
||
gtkglext
|
||
hdf5
|
||
ilmbase
|
||
imath ;should be propagated by openexr
|
||
jasper
|
||
libgphoto2
|
||
libjpeg-turbo
|
||
libpng
|
||
libtiff
|
||
libwebp
|
||
openblas
|
||
openexr
|
||
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")
|
||
(home-page "https://opencv.org/")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public vips
|
||
(package
|
||
(name "vips")
|
||
(version "8.10.6")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append
|
||
"https://github.com/libvips/libvips/releases/download/v"
|
||
version "/vips-" version ".tar.gz"))
|
||
(sha256
|
||
(base32 "0vjsh3i0861f6h9as3bch956cidz824zz499pvhjs3lfjn6hhs14"))))
|
||
(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
|
||
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 "3.0.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://gmic.eu/files/source/gmic_"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32 "080inz0wisv3rhvbnzrgcs3j25wq86gybp68yi56gw6vwswnn19z"))))
|
||
(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
|
||
;;opencv ;OpenCV is currently broken in the CI
|
||
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))
|
||
(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-krita
|
||
(package
|
||
(inherit gmic-qt)
|
||
(name "gmic-qt-krita")
|
||
(arguments
|
||
(substitute-keyword-arguments (package-arguments gmic-qt)
|
||
((#:configure-flags flags)
|
||
'(list "-DGMIC_QT_HOST=krita" "-DENABLE_DYNAMIC_LINKING=ON"
|
||
(string-append "-DGMIC_LIB_PATH="
|
||
(assoc-ref %build-inputs "gmic") "/lib")))))
|
||
(synopsis "Krita plugin for the G'MIC image processing framework")))
|
||
|
||
(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
|
||
`(("vips" ,vips)
|
||
("glib" ,glib)
|
||
("libtiff" ,libtiff)
|
||
("gtk+-2" ,gtk+-2)
|
||
("libxml2" ,libxml2)
|
||
("libexif" ,libexif)
|
||
("libjpeg" ,libjpeg-turbo) ;required by vips.pc
|
||
("librsvg" ,librsvg)
|
||
("fftw" ,fftw)
|
||
("libgsf" ,libgsf)
|
||
("imagemagick" ,imagemagick)
|
||
("orc" ,orc)
|
||
("matio" ,matio)
|
||
("lcms" ,lcms)
|
||
("libwebp" ,libwebp)
|
||
("openexr" ,openexr-2)
|
||
("poppler" ,poppler)
|
||
("gsl" ,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 vxl
|
||
(package
|
||
(name "vxl")
|
||
(version "2.0.2")
|
||
(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 "0949hw57szq8943f1whwqaz591xjmb19kj803hcv74hdai2b0ycg"))
|
||
(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)
|
||
(arguments
|
||
`(#:tests? #f ; tests require network access and external data
|
||
#:configure-flags
|
||
'("-DITK_USE_GPU=ON"
|
||
"-DITK_USE_SYSTEM_LIBRARIES=ON"
|
||
"-DITK_USE_SYSTEM_GOOGLETEST=ON"
|
||
"-DITK_BUILD_SHARED=ON"
|
||
;; 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")
|
||
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'do-not-tune
|
||
(lambda _
|
||
(substitute* "CMake/ITKSetStandardCompilerFlags.cmake"
|
||
(("-mute=native") ""))
|
||
#t)))))
|
||
(inputs
|
||
`(("eigen" ,eigen)
|
||
("expat" ,expat)
|
||
("fftw" ,fftw)
|
||
("fftwf" ,fftwf)
|
||
("hdf5" ,hdf5)
|
||
("libjpeg" ,libjpeg-turbo)
|
||
("libpng" ,libpng)
|
||
("libtiff" ,libtiff)
|
||
("mesa" ,mesa-opencl)
|
||
("perl" ,perl)
|
||
("python" ,python)
|
||
("tbb" ,tbb)
|
||
("vxl" ,vxl-1)
|
||
("zlib" ,zlib)))
|
||
(native-inputs
|
||
(list googletest pkg-config))
|
||
(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"))))
|
||
(arguments
|
||
`(#: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")))))
|
||
|
||
(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"))))))
|
||
|
||
(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"))))))))))
|
||
(inputs
|
||
(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)
|
||
("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)
|
||
(inputs
|
||
`(("giflib" ,giflib)
|
||
("libjpeg" ,libjpeg-turbo)
|
||
("libpng" ,libpng)
|
||
("perl" ,perl)))
|
||
(native-inputs
|
||
`(("pkg-config" ,pkg-config)
|
||
("docbook-xml" ,docbook-xml)
|
||
("docbook-xsl" ,docbook-xsl)
|
||
("xsltproc" ,libxslt)))
|
||
(arguments
|
||
`(#:tests? #f ; No tests.
|
||
#:make-flags (list
|
||
(string-append "PREFIX=" (assoc-ref %outputs "out"))
|
||
(string-append "MANPAGE_XSL="
|
||
(assoc-ref %build-inputs "docbook-xsl")
|
||
"/xml/xsl/docbook-xsl-*/manpages/docbook.xsl"))
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(delete 'configure)
|
||
(add-before 'install 'make-local-docbook-xml
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
(substitute* "metapixel.xml"
|
||
(("http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd")
|
||
(string-append (assoc-ref inputs "docbook-xml")
|
||
"/xml/dtd/docbook/docbookx.dtd")))
|
||
#t))
|
||
(add-before 'install 'fix-directory-creation
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(mkdir-p (string-append (assoc-ref outputs "out") "/share/man/man1"))
|
||
#t)))))
|
||
(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))
|
||
(inputs
|
||
`(("boost" ,boost)
|
||
("libjpeg" ,libjpeg-turbo)
|
||
("libpng" ,libpng)
|
||
("libtiff" ,libtiff)
|
||
("qtbase" ,qtbase-5)
|
||
("qtsvg" ,qtsvg)
|
||
("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"))))
|
||
(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 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+)))
|