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504c285d JD |
1 | ;;; GNU Guix --- Functional package management for GNU |
2 | ;;; Copyright © 2017 John Darrington <jmd@gnu.org> | |
18696f7a | 3 | ;;; Copyright © 2017, 2019 Ricardo Wurmus <rekado@elephly.net> |
e025de68 | 4 | ;;; Copyright © 2014, 2021 Ludovic Courtès <ludo@gnu.org> |
fb226b43 JD |
5 | ;;; Copyright © 2014 Mark H Weaver <mhw@netris.org> |
6 | ;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.org> | |
cc33f50d | 7 | ;;; Copyright © 2018–2021 Tobias Geerinckx-Rice <me@tobias.gr> |
62834314 | 8 | ;;; Copyright © 2018 Björn Höfling <bjoern.hoefling@bjoernhoefling.de> |
e506b5e9 | 9 | ;;; Copyright © 2018 Lprndn <guix@lprndn.info> |
b17b5411 | 10 | ;;; Copyright © 2019, 2021 Efraim Flashner <efraim@flashner.co.il> |
957e0be3 | 11 | ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com> |
5dc130c4 | 12 | ;;; Copyright © 2020, 2021 Vinicius Monego <monego@posteo.net> |
85c4f486 | 13 | ;;; Copyright © 2020 Pierre Neidhardt <mail@ambrevar.xyz> |
a76e9d13 | 14 | ;;; Copyright © 2020 Brendan Tildesley <mail@brendan.scot> |
58a5746e | 15 | ;;; Copyright © 2021 Oleh Malyi <astroclubzp@gmail.com> |
251b0f7a | 16 | ;;; Copyright © 2021 Felix Gruber <felgru@posteo.net> |
48f7aa1c | 17 | ;;; Copyright © 2021 Andy Tai <atai@atai.org> |
950475bb | 18 | ;;; Copyright © 2021 Ekaitz Zarraga <ekaitz@elenq.tech> |
504c285d JD |
19 | ;;; |
20 | ;;; This file is part of GNU Guix. | |
21 | ;;; | |
22 | ;;; GNU Guix is free software; you can redistribute it and/or modify it | |
23 | ;;; under the terms of the GNU General Public License as published by | |
24 | ;;; the Free Software Foundation; either version 3 of the License, or (at | |
25 | ;;; your option) any later version. | |
26 | ;;; | |
27 | ;;; GNU Guix is distributed in the hope that it will be useful, but | |
28 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of | |
29 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
30 | ;;; GNU General Public License for more details. | |
31 | ;;; | |
32 | ;;; You should have received a copy of the GNU General Public License | |
33 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. | |
34 | ||
35 | (define-module (gnu packages image-processing) | |
36 | #:use-module ((guix licenses) #:prefix license:) | |
37 | #:use-module (guix packages) | |
38 | #:use-module (guix utils) | |
39 | #:use-module (guix download) | |
6c56e9c4 | 40 | #:use-module (guix git-download) |
a76e9d13 | 41 | #:use-module (guix build-system qt) |
cdb2a211 | 42 | #:use-module (guix build-system cmake) |
504c285d JD |
43 | #:use-module (guix build-system gnu) |
44 | #:use-module (gnu packages) | |
cdb2a211 | 45 | #:use-module (gnu packages algebra) |
e506b5e9 | 46 | #:use-module (gnu packages bison) |
cdb2a211 | 47 | #:use-module (gnu packages boost) |
d7701e1b | 48 | #:use-module (gnu packages check) |
504c285d | 49 | #:use-module (gnu packages compression) |
1c4e6aa9 | 50 | #:use-module (gnu packages curl) |
85c4f486 | 51 | #:use-module (gnu packages docbook) |
504c285d | 52 | #:use-module (gnu packages documentation) |
e506b5e9 | 53 | #:use-module (gnu packages flex) |
fb226b43 | 54 | #:use-module (gnu packages fontutils) |
02e1acfb | 55 | #:use-module (gnu packages geo) |
5bbd6931 | 56 | #:use-module (gnu packages ghostscript) |
fb226b43 | 57 | #:use-module (gnu packages gl) |
5bbd6931 | 58 | #:use-module (gnu packages glib) |
cdb2a211 JD |
59 | #:use-module (gnu packages gnome) |
60 | #:use-module (gnu packages graphics) | |
61 | #:use-module (gnu packages graphviz) | |
5bbd6931 | 62 | #:use-module (gnu packages gstreamer) |
62834314 | 63 | #:use-module (gnu packages gtk) |
5d0f394b | 64 | #:use-module (gnu packages icu4c) |
504c285d | 65 | #:use-module (gnu packages image) |
5bbd6931 | 66 | #:use-module (gnu packages imagemagick) |
cdb2a211 | 67 | #:use-module (gnu packages maths) |
5bbd6931 | 68 | #:use-module (gnu packages pdf) |
cdb2a211 | 69 | #:use-module (gnu packages perl) |
62834314 | 70 | #:use-module (gnu packages photo) |
cdb2a211 | 71 | #:use-module (gnu packages pkg-config) |
62834314 | 72 | #:use-module (gnu packages protobuf) |
cdb2a211 | 73 | #:use-module (gnu packages python) |
44d10b1f | 74 | #:use-module (gnu packages python-xyz) |
1c4e6aa9 | 75 | #:use-module (gnu packages qt) |
fb226b43 | 76 | #:use-module (gnu packages serialization) |
a675c01f | 77 | #:use-module (gnu packages sqlite) |
d7701e1b | 78 | #:use-module (gnu packages tbb) |
8486a80d | 79 | #:use-module (gnu packages tls) |
2283cf4c | 80 | #:use-module (gnu packages version-control) |
62834314 | 81 | #:use-module (gnu packages video) |
fb226b43 | 82 | #:use-module (gnu packages xiph) |
cdb2a211 | 83 | #:use-module (gnu packages xml) |
ebe0271a | 84 | #:use-module (gnu packages xorg) |
18696f7a RW |
85 | #:use-module (ice-9 match) |
86 | #:use-module (srfi srfi-1)) | |
504c285d | 87 | |
504c285d JD |
88 | (define-public dcmtk |
89 | (package | |
90 | (name "dcmtk") | |
5d0f394b | 91 | (version "3.6.6") |
882d579d TGR |
92 | (source |
93 | (origin | |
94 | (method url-fetch) | |
95 | (uri | |
96 | (string-append "ftp://dicom.offis.de/pub/dicom/offis/software/dcmtk/" | |
97 | "dcmtk" (string-join (string-split version #\.) "") | |
98 | "/dcmtk-" version ".tar.gz")) | |
99 | (sha256 | |
5d0f394b | 100 | (base32 "13j5yf3p6qj3mr17d77r3kcqchf055hgvk1w15vmdr8f54mwcnb8")))) |
882d579d | 101 | (build-system cmake-build-system) |
504c285d | 102 | (inputs |
5d0f394b | 103 | `(("icu4c" ,icu4c) |
4bd428a7 | 104 | ("libjpeg" ,libjpeg-turbo) |
504c285d | 105 | ("libpng" ,libpng) |
882d579d | 106 | ("libtiff" ,libtiff) |
8486a80d TGR |
107 | ("libxml2" ,libxml2) |
108 | ("openssl" ,openssl) | |
504c285d JD |
109 | ("zlib" ,zlib))) |
110 | (native-inputs | |
882d579d | 111 | `(("doxygen" ,doxygen))) ; for HTML documentation |
d2ad4f2e | 112 | (home-page "https://dcmtk.org") |
504c285d JD |
113 | (synopsis "Libraries and programs implementing parts of the DICOM standard") |
114 | (description "DCMTK is a collection of libraries and applications | |
115 | implementing large parts the DICOM standard. It includes software for | |
116 | examining, constructing and converting DICOM image files, handling offline | |
117 | media, sending and receiving images over a network connection, as well as | |
118 | demonstrative image storage and worklist servers.") | |
119 | (license (license:fsf-free | |
120 | "file://COPYRIGHT" | |
121 | "A union of the Apache 2.0 licence and various non-copyleft | |
122 | licences similar to the Modified BSD licence.")))) | |
cdb2a211 JD |
123 | |
124 | (define-public mia | |
125 | (package | |
126 | (name "mia") | |
11861d2b | 127 | (version "2.4.6") |
cdb2a211 JD |
128 | (source (origin |
129 | (method url-fetch) | |
130 | (uri (string-append "mirror://sourceforge/mia/mia/" | |
131 | (version-major+minor version) | |
132 | "/mia-" version ".tar.xz")) | |
133 | (sha256 | |
134 | (base32 | |
11861d2b | 135 | "0j4nd5z7i3v199jh7hqqhwd4g7snchizkc7rhzanpvngqg91m1pb")))) |
cdb2a211 JD |
136 | (build-system cmake-build-system) |
137 | (arguments | |
138 | `(#:configure-flags | |
139 | (list "-DMIA_CREATE_NIPYPE_INTERFACES=0" | |
cdb2a211 JD |
140 | "-DCMAKE_CXX_FLAGS=-fpermissive"))) |
141 | (inputs | |
142 | `(("boost" ,boost) | |
143 | ("dcmtk" ,dcmtk) | |
144 | ("doxygen" ,doxygen) | |
145 | ("eigen" ,eigen) | |
146 | ("fftw" ,fftw) | |
147 | ("fftwf" ,fftwf) | |
148 | ("gsl" ,gsl) | |
149 | ("gts" ,gts) | |
150 | ("hdf5" ,hdf5) | |
151 | ("itpp" ,itpp) | |
4bd428a7 | 152 | ("libjpeg" ,libjpeg-turbo) |
cdb2a211 JD |
153 | ("libpng" ,libpng) |
154 | ("libtiff" ,libtiff) | |
155 | ("libxml" ,libxml2) | |
156 | ("libxml++" ,libxml++) | |
157 | ("maxflow" ,maxflow) | |
158 | ("niftilib" ,niftilib) | |
159 | ("nlopt" ,nlopt) | |
160 | ("openexr" ,openexr) | |
161 | ("python-lxml" ,python2-lxml) | |
162 | ("vtk" ,vtk))) | |
163 | (native-inputs | |
164 | `(("pkg-config" ,pkg-config) | |
165 | ("python" ,python-2))) | |
166 | (home-page "http://mia.sourceforge.net") | |
167 | (synopsis "Toolkit for gray scale medical image analysis") | |
168 | (description "MIA provides a combination of command line tools, plug-ins, | |
169 | and libraries that make it possible run image processing tasks interactively | |
170 | in a command shell and to prototype using the shell's scripting language. It | |
171 | is built around a plug-in structure that makes it easy to add functionality | |
172 | without compromising the original code base and it makes use of a wide variety | |
173 | of external libraries that provide additional functionality.") | |
174 | (license license:gpl3+))) | |
fb226b43 | 175 | |
2283cf4c TGR |
176 | (define-public opencolorio |
177 | (package | |
178 | (name "opencolorio") | |
179 | (version "1.1.1") | |
180 | (source | |
181 | (origin | |
182 | (method git-fetch) | |
183 | (uri (git-reference | |
184 | (url "https://github.com/AcademySoftwareFoundation/OpenColorIO") | |
185 | (commit (string-append "v" version)))) | |
186 | (sha256 | |
187 | (base32 "12srvxca51czpfjl0gabpidj9n84mw78ivxy5w75qhq2mmc798sb")) | |
188 | (file-name (git-file-name name version)) | |
189 | (modules '((guix build utils))) | |
190 | (snippet | |
191 | `(begin | |
192 | ;; Remove bundled tarballs, patches, and .jars(!). XXX: Upstream | |
193 | ;; claims to have fixed USE_EXTERNAL_YAML, but it still fails with: | |
194 | ;; https://github.com/AcademySoftwareFoundation/OpenColorIO/issues/517 | |
195 | ;; When removing it, also remove it from the licence field comment. | |
196 | (for-each delete-file-recursively | |
197 | (filter | |
198 | (lambda (full-name) | |
199 | (let ((file (basename full-name))) | |
200 | (not (or (string-prefix? "yaml-cpp-0.3" file) | |
201 | (string=? "unittest.h" file))))) | |
202 | (find-files "ext" ".*"))) | |
203 | ||
204 | #t)))) | |
205 | (build-system cmake-build-system) | |
206 | (arguments | |
207 | `(#:configure-flags | |
208 | (list (string-append "-DCMAKE_CXX_FLAGS=" | |
209 | "-Wno-error=deprecated-declarations " | |
210 | "-Wno-error=unused-function") | |
211 | "-DOCIO_BUILD_STATIC=OFF" | |
212 | ;; "-DUSE_EXTERNAL_YAML=ON" | |
213 | "-DUSE_EXTERNAL_TINYXML=ON" | |
214 | "-DUSE_EXTERNAL_LCMS=ON") | |
215 | #:phases | |
216 | (modify-phases %standard-phases | |
217 | (add-after 'unpack 'patch-test-suite | |
218 | (lambda _ | |
219 | (substitute* "src/core_tests/CMakeLists.txt" | |
220 | (("/bin/sh") (which "bash"))) | |
221 | #t))))) | |
222 | (native-inputs | |
223 | `(("git" ,git) | |
224 | ("pkg-config" ,pkg-config))) | |
225 | (inputs | |
226 | ;; XXX Adding freeglut, glew, ilmbase, mesa, and openimageio for | |
227 | ;; ocioconvert fails: error: conflicting declaration ?typedef void | |
228 | ;; (* PFNGLGETFRAGMENTMATERIALFVSGIXPROC)(GLenum, GLenum, GLfloat*) | |
229 | `(("lcms" ,lcms) | |
230 | ("openexr" ,openexr) | |
231 | ("tinyxml" ,tinyxml))) | |
232 | (home-page "https://opencolorio.org") | |
233 | (synopsis "Color management for visual effects and animation") | |
234 | (description | |
235 | "OpenColorIO, or OCIO, is a complete color management solution geared | |
236 | towards motion picture production, with an emphasis on visual effects and | |
237 | computer animation. It provides a straightforward and consistent user | |
238 | experience across all supporting applications while allowing for sophisticated | |
239 | back-end configuration options suitable for high-end production usage. | |
240 | ||
241 | OCIO is compatible with the @acronym{ACES, Academy Color Encoding | |
242 | Specification} and is @acronym{LUT, look-up table}-format agnostic, supporting | |
243 | many popular formats.") | |
244 | (license (list license:expat ; docs/ociotheme/static, ext/yaml-cpp-* | |
245 | license:zlib ; src/core/md5 | |
246 | license:bsd-3)))) ; the rest | |
247 | ||
fb226b43 JD |
248 | (define-public vtk |
249 | (package | |
250 | (name "vtk") | |
48f7aa1c | 251 | (version "9.0.1") |
fb226b43 JD |
252 | (source (origin |
253 | (method url-fetch) | |
f1d4f264 | 254 | (uri (string-append "https://vtk.org/files/release/" |
fb226b43 JD |
255 | (version-major+minor version) |
256 | "/VTK-" version ".tar.gz")) | |
257 | (sha256 | |
258 | (base32 | |
48f7aa1c | 259 | "1ir2lq9i45ls374lcmjzw0nrm5l5hnm1w47lg8g8d0n2j7hsaf8v")) |
251b0f7a FG |
260 | (patches |
261 | (search-patches "vtk-fix-freetypetools-build-failure.patch")) | |
b17b5411 EF |
262 | (modules '((guix build utils))) |
263 | (snippet | |
264 | '(begin | |
265 | (for-each | |
266 | (lambda (dir) | |
267 | (delete-file-recursively | |
268 | (string-append "ThirdParty/" dir "/vtk" dir))) | |
48f7aa1c | 269 | ;; pugixml depended upon unconditionally |
a675c01f EF |
270 | '("doubleconversion" "eigen" "expat" "freetype" "gl2ps" |
271 | "glew" "hdf5" "jpeg" "jsoncpp" "libproj" "libxml2" "lz4" | |
48f7aa1c | 272 | "netcdf" "ogg" "png" "sqlite" "theora" "tiff" "zlib")) |
b17b5411 | 273 | #t)))) |
e025de68 | 274 | (properties `((release-monitoring-url . "https://vtk.org/download/"))) |
fb226b43 JD |
275 | (build-system cmake-build-system) |
276 | (arguments | |
277 | '(#:build-type "Release" ;Build without '-g' to save space. | |
a675c01f | 278 | #:configure-flags '(;"-DBUILD_TESTING:BOOL=TRUE" |
48f7aa1c AT |
279 | ; ; not honored |
280 | "-DVTK_USE_EXTERNAL=OFF" ;; default | |
281 | "-DVTK_MODULE_USE_EXTERNAL_VTK_doubleconversion=ON" | |
282 | "-DVTK_MODULE_USE_EXTERNAL_VTK_eigen=ON" | |
283 | "-DVTK_MODULE_USE_EXTERNAL_VTK_expat=ON" | |
284 | "-DVTK_MODULE_USE_EXTERNAL_VTK_freetype=ON" | |
285 | "-DVTK_MODULE_USE_EXTERNAL_VTK_gl2ps=ON" | |
286 | "-DVTK_MODULE_USE_EXTERNAL_VTK_glew=ON" | |
287 | "-DVTK_MODULE_USE_EXTERNAL_VTK_hdf5=ON" | |
288 | "-DVTK_MODULE_USE_EXTERNAL_VTK_jpeg=ON" | |
289 | "-DVTK_MODULE_USE_EXTERNAL_VTK_jsoncpp=ON" | |
290 | "-DVTK_MODULE_USE_EXTERNAL_VTK_libproj=ON" | |
291 | "-DVTK_MODULE_USE_EXTERNAL_VTK_libxml2=ON" | |
292 | "-DVTK_MODULE_USE_EXTERNAL_VTK_lz4=ON" | |
293 | "-DVTK_MODULE_USE_EXTERNAL_VTK_netcdf=ON" | |
294 | "-DVTK_MODULE_USE_EXTERNAL_VTK_ogg=ON" | |
295 | "-DVTK_MODULE_USE_EXTERNAL_VTK_png=ON" | |
296 | ;"-DVTK_MODULE_USE_EXTERNAL_VTK_pugixml=ON" ; breaks IO/CityGML | |
297 | "-DVTK_MODULE_USE_EXTERNAL_VTK_sqlite=ON" | |
298 | "-DVTK_MODULE_USE_EXTERNAL_VTK_theora=ON" | |
299 | "-DVTK_MODULE_USE_EXTERNAL_VTK_tiff=ON" | |
300 | "-DVTK_MODULE_USE_EXTERNAL_VTK_zlib=ON" | |
301 | ) | |
302 | #:phases | |
303 | (modify-phases %standard-phases | |
304 | (add-after 'unpack 'patch-sources | |
305 | (lambda _ | |
306 | (substitute* "Common/Core/vtkFloatingPointExceptions.cxx" | |
307 | (("<fenv.h>") "<cfenv>")) | |
308 | (substitute* "Common/Core/CMakeLists.txt" | |
309 | (("fenv.h") "cfenv"))))) | |
a675c01f | 310 | #:tests? #f)) ;XXX: test data not included |
fb226b43 | 311 | (inputs |
a675c01f EF |
312 | `(("double-conversion" ,double-conversion) |
313 | ("eigen" ,eigen) | |
314 | ("expat" ,expat) | |
fb226b43 | 315 | ("freetype" ,freetype) |
a675c01f EF |
316 | ("gl2ps" ,gl2ps) |
317 | ("glew" ,glew) | |
fac4e4ae | 318 | ("glu" ,glu) |
fb226b43 | 319 | ("hdf5" ,hdf5) |
4bd428a7 | 320 | ("jpeg" ,libjpeg-turbo) |
fb226b43 | 321 | ("jsoncpp" ,jsoncpp) |
fb226b43 | 322 | ("libtheora" ,libtheora) |
fac4e4ae EF |
323 | ("libX11" ,libx11) |
324 | ("libxml2" ,libxml2) | |
325 | ("libXt" ,libxt) | |
a675c01f | 326 | ("lz4" ,lz4) |
fac4e4ae | 327 | ("mesa" ,mesa) |
a675c01f | 328 | ("netcdf" ,netcdf) |
fb226b43 | 329 | ("png" ,libpng) |
a675c01f EF |
330 | ("proj" ,proj.4) |
331 | ;("pugixml" ,pugixml) | |
332 | ("sqlite" ,sqlite) | |
fb226b43 | 333 | ("tiff" ,libtiff) |
fac4e4ae | 334 | ("xorgproto" ,xorgproto) |
fb226b43 | 335 | ("zlib" ,zlib))) |
48f7aa1c AT |
336 | (propagated-inputs |
337 | ;; VTK's 'VTK-vtk-module-find-packages.cmake' calls | |
338 | ;; 'find_package(THEORA)', which in turns looks for libogg. | |
339 | `(("libogg" ,libogg))) | |
f1d4f264 | 340 | (home-page "https://vtk.org/") |
fb226b43 JD |
341 | (synopsis "Libraries for 3D computer graphics") |
342 | (description | |
343 | "The Visualization Toolkit (VTK) is a C++ library for 3D computer graphics, | |
344 | image processing and visualization. It supports a wide variety of | |
345 | visualization algorithms including: scalar, vector, tensor, texture, and | |
346 | volumetric methods; and advanced modeling techniques such as: implicit | |
347 | modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay | |
348 | triangulation. VTK has an extensive information visualization framework, has | |
349 | a suite of 3D interaction widgets, supports parallel processing, and | |
350 | integrates with various databases on GUI toolkits such as Qt and Tk.") | |
351 | (license license:bsd-3))) | |
62834314 | 352 | |
950475bb EZ |
353 | ;; freecad needs an old version of VTK, because VTK's API changed from 8 to 9 |
354 | (define-public vtk-8 | |
355 | (package (inherit vtk) | |
356 | (version "8.2.0") | |
357 | (source (origin | |
358 | (method url-fetch) | |
359 | (uri (string-append "https://vtk.org/files/release/" | |
360 | (version-major+minor version) | |
361 | "/VTK-" version ".tar.gz")) | |
362 | (sha256 | |
363 | (base32 | |
364 | "1fspgp8k0myr6p2a6wkc21ldcswb4bvmb484m12mxgk1a9vxrhrl")))) | |
365 | (inputs | |
366 | `(("jsoncpp" ,jsoncpp-for-tensorflow) | |
367 | ,@(alist-delete "jsoncpp" (package-inputs vtk)))))) | |
368 | ||
18696f7a RW |
369 | ;; itksnap needs an older variant of VTK. |
370 | (define-public vtk-6 | |
371 | (package (inherit vtk) | |
372 | (version "6.3.0") | |
373 | (source (origin | |
374 | (method url-fetch) | |
375 | (uri (string-append "https://vtk.org/files/release/" | |
376 | (version-major+minor version) | |
377 | "/VTK-" version ".tar.gz")) | |
378 | (sha256 | |
379 | (base32 | |
380 | "0pla1r5mvkgl4sl213gfdhzrypdgai0h3z5mfgm6p9jz9hsr794j")))) | |
381 | (inputs | |
382 | `(("jsoncpp" ,jsoncpp-for-tensorflow) | |
383 | ,@(alist-delete "jsoncpp" (package-inputs vtk)))))) | |
384 | ||
62834314 BH |
385 | (define-public opencv |
386 | (package | |
387 | (name "opencv") | |
63856931 | 388 | (version "3.4.3") |
62834314 | 389 | (source (origin |
6c56e9c4 EF |
390 | (method git-fetch) |
391 | (uri (git-reference | |
392 | (url "https://github.com/opencv/opencv") | |
393 | (commit version))) | |
394 | (file-name (git-file-name name version)) | |
62834314 BH |
395 | (sha256 |
396 | (base32 | |
6c56e9c4 | 397 | "06bc61r8myym4s8im10brdjfg4wxkrvsbhhl7vr1msdan2xddzi3")) |
8bf70426 TGR |
398 | (patches |
399 | (search-patches "opencv-fix-build-of-grfmt_jpeg2000.cpp.patch")) | |
62834314 BH |
400 | (modules '((guix build utils))) |
401 | (snippet | |
402 | '(begin | |
403 | ;; Remove external libraries. We have all available in Guix: | |
404 | (delete-file-recursively "3rdparty") | |
405 | ||
406 | ;; Milky icon set is non-free: | |
407 | (delete-file-recursively "modules/highgui/src/files_Qt/Milky") | |
408 | ||
409 | ;; Some jars found: | |
410 | (for-each delete-file | |
411 | '("modules/java/test/pure_test/lib/junit-4.11.jar" | |
6c56e9c4 EF |
412 | "samples/java/sbt/sbt/sbt-launch.jar")) |
413 | #t)))) | |
62834314 BH |
414 | (build-system cmake-build-system) |
415 | (arguments | |
416 | `(#:configure-flags | |
417 | (list "-DWITH_IPP=OFF" | |
418 | "-DWITH_ITT=OFF" | |
6949f45c | 419 | "-DWITH_CAROTENE=OFF" ; only visible on arm/aarch64 |
fdeb2def | 420 | "-DENABLE_PRECOMPILED_HEADERS=OFF" |
62834314 BH |
421 | |
422 | ;; CPU-Features: | |
423 | ;; See cmake/OpenCVCompilerOptimizations.cmake | |
424 | ;; (CPU_ALL_OPTIMIZATIONS) for a list of all optimizations | |
425 | ;; BASELINE is the minimum optimization all CPUs must support | |
426 | ;; | |
ebe0271a EF |
427 | ;; DISPATCH is the list of optional dispatches. |
428 | "-DCPU_BASELINE=SSE2" | |
62834314 | 429 | |
ebe0271a EF |
430 | ,@(match (%current-system) |
431 | ("x86_64-linux" | |
432 | '("-DCPU_DISPATCH=NEON;VFPV3;FP16;SSE;SSE2;SSE3;SSSE3;SSE4_1;SSE4_2;POPCNT;AVX;FP16;AVX2;FMA3;AVX_512F;AVX512_SKX" | |
433 | "-DCPU_DISPATCH_REQUIRE=SSE3,SSSE3,SSE4_1,SSE4_2,AVX,AVX2")) | |
434 | ("armhf-linux" | |
435 | '("-DCPU_BASELINE_DISABLE=NEON")) ; causes build failures | |
436 | ("aarch64-linux" | |
437 | '("-DCPU_BASELINE=NEON" | |
438 | "-DCPU_DISPATCH=NEON;VFPV3;FP16")) | |
439 | (_ '())) | |
62834314 BH |
440 | |
441 | "-DBUILD_PERF_TESTS=OFF" | |
6949f45c | 442 | "-DBUILD_TESTS=ON" |
62834314 | 443 | |
b5baf952 | 444 | (string-append "-DOPENCV_EXTRA_MODULES_PATH=" (getcwd) |
6c56e9c4 | 445 | "/opencv-contrib/modules") |
62834314 BH |
446 | |
447 | ;;Define test data: | |
b5baf952 | 448 | (string-append "-DOPENCV_TEST_DATA_PATH=" (getcwd) |
6c56e9c4 | 449 | "/opencv-extra/testdata") |
62834314 BH |
450 | |
451 | ;; Is ON by default and would try to rebuild 3rd-party protobuf, | |
452 | ;; which we had removed, which would lead to an error: | |
453 | "-DBUILD_PROTOBUF=OFF" | |
454 | ||
455 | ;; Rebuild protobuf files, because we have a slightly different | |
456 | ;; version than the included one. If we would not update, we | |
457 | ;; would get a compile error later: | |
458 | "-DPROTOBUF_UPDATE_FILES=ON" | |
459 | ||
460 | ;; xfeatures2d disabled, because it downloads extra binaries from | |
461 | ;; https://github.com/opencv/opencv_3rdparty | |
462 | ;; defined in xfeatures2d/cmake/download_{vgg|bootdesc}.cmake | |
463 | ;; Cmp this bug entry: | |
464 | ;; https://github.com/opencv/opencv_contrib/issues/1131 | |
465 | "-DBUILD_opencv_xfeatures2d=OFF") | |
466 | #:phases | |
467 | (modify-phases %standard-phases | |
468 | (add-after 'unpack 'disable-broken-tests | |
469 | (lambda _ | |
470 | ;; These tests fails with: | |
471 | ;; vtkXOpenGLRenderWindow (0x723990): Could not find a decent config | |
472 | ;; I think we have no OpenGL support with the Xvfb. | |
473 | (substitute* '("modules/viz/test/test_tutorial3.cpp" | |
474 | "modules/viz/test/test_main.cpp" | |
475 | "modules/viz/test/tests_simple.cpp" | |
476 | "modules/viz/test/test_viz3d.cpp") | |
477 | (("(TEST\\(Viz, )([a-z].*\\).*)" all pre post) | |
478 | (string-append pre "DISABLED_" post))) | |
479 | ||
480 | ;; This one fails with "unknown file: Failure" | |
481 | ;; But I couldn't figure out which file was missing: | |
6c56e9c4 | 482 | (substitute* "../opencv-contrib/modules/face/test/test_face_align.cpp" |
62834314 BH |
483 | (("(TEST\\(CV_Face_FacemarkKazemi, )(can_detect_landmarks\\).*)" |
484 | all pre post) | |
485 | (string-append pre "DISABLED_" post))) | |
486 | ||
487 | ;; Failure reason: Bad accuracy | |
488 | ;; Incorrect count of accurate poses [2nd case]: 90.000000 / 94.000000 | |
6c56e9c4 | 489 | (substitute* "../opencv-contrib/modules/rgbd/test/test_odometry.cpp" |
62834314 BH |
490 | (("(TEST\\(RGBD_Odometry_Rgbd, )(algorithmic\\).*)" all pre post) |
491 | (string-append pre "DISABLED_" post))) | |
492 | #t)) | |
493 | ||
62834314 BH |
494 | (add-after 'unpack 'unpack-submodule-sources |
495 | (lambda* (#:key inputs #:allow-other-keys) | |
496 | (mkdir "../opencv-extra") | |
497 | (mkdir "../opencv-contrib") | |
6c56e9c4 EF |
498 | (copy-recursively (assoc-ref inputs "opencv-extra") |
499 | "../opencv-extra") | |
500 | (invoke "tar" "xvf" | |
501 | (assoc-ref inputs "opencv-contrib") | |
502 | "--strip-components=1" | |
503 | "-C" "../opencv-contrib"))) | |
62834314 BH |
504 | |
505 | (add-after 'set-paths 'add-ilmbase-include-path | |
506 | (lambda* (#:key inputs #:allow-other-keys) | |
507 | ;; OpenEXR propagates ilmbase, but its include files do not appear | |
508 | ;; in the CPATH, so we need to add "$ilmbase/include/OpenEXR/" to | |
509 | ;; the CPATH to satisfy the dependency on "ImathVec.h". | |
510 | (setenv "CPATH" | |
511 | (string-append (assoc-ref inputs "ilmbase") | |
512 | "/include/OpenEXR" | |
513 | ":" (or (getenv "CPATH") ""))) | |
514 | #t)) | |
515 | (add-before 'check 'start-xserver | |
516 | (lambda* (#:key inputs #:allow-other-keys) | |
517 | (let ((xorg-server (assoc-ref inputs "xorg-server")) | |
518 | (disp ":1")) | |
519 | (setenv "HOME" (getcwd)) | |
520 | (setenv "DISPLAY" disp) | |
521 | ;; There must be a running X server and make check doesn't start one. | |
522 | ;; Therefore we must do it. | |
523 | (zero? (system (format #f "~a/bin/Xvfb ~a &" xorg-server disp))))))))) | |
524 | (native-inputs | |
6c56e9c4 | 525 | `(("pkg-config" ,pkg-config) |
ff337525 | 526 | ("xorg-server" ,xorg-server-for-tests) ; For running the tests |
62834314 BH |
527 | ("opencv-extra" |
528 | ,(origin | |
6c56e9c4 EF |
529 | (method git-fetch) |
530 | (uri (git-reference | |
531 | (url "https://github.com/opencv/opencv_extra") | |
532 | (commit version))) | |
533 | (file-name (git-file-name "opencv_extra" version)) | |
62834314 | 534 | (sha256 |
6c56e9c4 | 535 | (base32 "08p5xnq8n1jw8svvz0fnirfg7q8dm3p4a5dl7527s5xj0f9qn7lp")))) |
62834314 BH |
536 | ("opencv-contrib" |
537 | ,(origin | |
6c56e9c4 EF |
538 | (method git-fetch) |
539 | (uri (git-reference | |
540 | (url "https://github.com/opencv/opencv_contrib") | |
541 | (commit version))) | |
542 | (file-name (git-file-name "opencv_contrib" version)) | |
8e21fa0b | 543 | (patches (search-patches "opencv-rgbd-aarch64-test-fix.patch")) |
62834314 | 544 | (sha256 |
6c56e9c4 | 545 | (base32 "1f334glf39nk42mpqq6j732h3ql2mpz89jd4mcl678s8n73nfjh2")))))) |
4bd428a7 | 546 | (inputs `(("libjpeg" ,libjpeg-turbo) |
62834314 BH |
547 | ("libpng" ,libpng) |
548 | ("jasper" ,jasper) | |
549 | ;; ffmpeg 4.0 causes core dumps in tests. | |
550 | ("ffmpeg" ,ffmpeg-3.4) | |
551 | ("libtiff" ,libtiff) | |
552 | ("hdf5" ,hdf5) | |
553 | ("libgphoto2" ,libgphoto2) | |
554 | ("libwebp" ,libwebp) | |
555 | ("zlib" ,zlib) | |
556 | ("gtkglext" ,gtkglext) | |
557 | ("openexr" ,openexr) | |
558 | ("ilmbase" ,ilmbase) | |
559 | ("gtk+" ,gtk+-2) | |
560 | ("python-numpy" ,python-numpy) | |
561 | ("protobuf" ,protobuf) | |
562 | ("vtk" ,vtk) | |
563 | ("python" ,python))) | |
5834e4b7 BH |
564 | ;; These three CVEs are not a problem of OpenCV, see: |
565 | ;; https://github.com/opencv/opencv/issues/10998 | |
566 | (properties '((lint-hidden-cve . ("CVE-2018-7712" | |
567 | "CVE-2018-7713" | |
568 | "CVE-2018-7714")))) | |
62834314 BH |
569 | (synopsis "Computer vision library") |
570 | (description "OpenCV is a library aimed at | |
571 | real-time computer vision, including several hundred computer | |
572 | vision algorithms. It can be used to do things like: | |
573 | ||
574 | @itemize | |
575 | @item image and video input and output | |
576 | @item image and video processing | |
577 | @item displaying | |
578 | @item feature recognition | |
579 | @item segmentation | |
580 | @item facial recognition | |
581 | @item stereo vision | |
582 | @item structure from motion | |
583 | @item augmented reality | |
584 | @item machine learning | |
585 | @end itemize\n") | |
586 | (home-page "https://opencv.org/") | |
587 | (license license:bsd-3))) | |
5bbd6931 L |
588 | |
589 | (define-public vips | |
590 | (package | |
591 | (name "vips") | |
cc33f50d | 592 | (version "8.10.6") |
7e52321f TGR |
593 | (source |
594 | (origin | |
595 | (method url-fetch) | |
596 | (uri (string-append | |
597 | "https://github.com/libvips/libvips/releases/download/v" | |
598 | version "/vips-" version ".tar.gz")) | |
599 | (sha256 | |
cc33f50d | 600 | (base32 "0vjsh3i0861f6h9as3bch956cidz824zz499pvhjs3lfjn6hhs14")))) |
5bbd6931 L |
601 | (build-system gnu-build-system) |
602 | (native-inputs | |
5d99167a EF |
603 | `(("gobject-introspection" ,gobject-introspection) |
604 | ("pkg-config" ,pkg-config))) | |
5bbd6931 | 605 | (inputs |
5d99167a EF |
606 | `(("expat" ,expat) |
607 | ("fftw" ,fftw) | |
608 | ("giflib" ,giflib) | |
609 | ("glib" ,glib) | |
610 | ("hdf5" ,hdf5) | |
611 | ("imagemagick" ,imagemagick) | |
612 | ("lcms" ,lcms) | |
613 | ("libexif" ,libexif) | |
614 | ("libgsf" ,libgsf) | |
4bd428a7 | 615 | ("libjpeg" ,libjpeg-turbo) |
5bbd6931 L |
616 | ("libpng" ,libpng) |
617 | ("librsvg" ,librsvg) | |
618 | ("libtiff" ,libtiff) | |
5d99167a | 619 | ("libxml2" ,libxml2) |
5bbd6931 | 620 | ("libwebp" ,libwebp) |
5d99167a | 621 | ("matio" ,matio) |
5bbd6931 L |
622 | ("niftilib" ,niftilib) |
623 | ("openexr" ,openexr) | |
624 | ("orc" ,orc) | |
5d99167a EF |
625 | ("pango" ,pango) |
626 | ("poppler" ,poppler))) | |
5bbd6931 | 627 | (home-page "https://libvips.github.io/libvips/") |
85e2f212 | 628 | (synopsis "Multithreaded image processing system with low memory needs") |
37c1cf89 | 629 | (description |
85e2f212 TGR |
630 | "VIPS is a demand-driven, horizontally threaded image processing library. |
631 | It's particularly good at processing large images, working with colour, | |
632 | scientific analysis, and general research & development. | |
633 | ||
634 | Compared to most image processing libraries VIPS needs little RAM and runs | |
635 | quickly, especially on machines with more than one CPU core. This is primarily | |
636 | due to its architecture which automatically parallelises the image workflows.") | |
5bbd6931 | 637 | (license license:lgpl2.1+))) |
e506b5e9 | 638 | |
657f8535 VM |
639 | (define-public gmic |
640 | (package | |
641 | (name "gmic") | |
ce9fe5f9 | 642 | (version "2.9.7") |
657f8535 VM |
643 | (source |
644 | (origin | |
645 | (method url-fetch) | |
646 | (uri (string-append "https://gmic.eu/files/source/gmic_" | |
647 | version ".tar.gz")) | |
648 | (sha256 | |
ce9fe5f9 | 649 | (base32 "05kzaplsl5qvxs7v6g73q0lq8dii8g6v77ap609188m7gr43f9cl")))) |
657f8535 VM |
650 | (build-system cmake-build-system) |
651 | (arguments | |
75862a9e VM |
652 | `(#:tests? #f ;there are no tests |
653 | #:configure-flags '("-DBUILD_LIB_STATIC=OFF" | |
654 | "-DENABLE_DYNAMIC_LINKING=ON" | |
655 | "-DENABLE_LTO=ON") | |
656 | #:phases | |
657 | (modify-phases %standard-phases | |
658 | (add-before 'configure 'set-LDFLAGS | |
659 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
660 | (setenv "LDFLAGS" | |
661 | (string-append | |
662 | "-Wl,-rpath=" | |
663 | (assoc-ref outputs "out") "/lib"))))))) | |
657f8535 VM |
664 | (native-inputs |
665 | `(("pkg-config" ,pkg-config))) | |
666 | (inputs | |
667 | `(("curl" ,curl) | |
668 | ("fftw" ,fftw) | |
669 | ("graphicsmagick" ,graphicsmagick) | |
670 | ("libjpeg-turbo" ,libjpeg-turbo) | |
671 | ("libpng" ,libpng) | |
672 | ("libtiff" ,libtiff) | |
673 | ("libx11" ,libx11) | |
674 | ;;("opencv" ,opencv) ;OpenCV is currently broken in the CI | |
675 | ("openexr" ,openexr) | |
676 | ("zlib" ,zlib))) | |
677 | (home-page "https://gmic.eu/") | |
678 | (synopsis "Full-featured framework for digital image processing") | |
679 | (description "G'MIC is a full-featured framework for digital image | |
680 | processing. It provides several user interfaces to convert / manipulate | |
681 | / filter / visualize generic image datasets, ranging from 1D scalar | |
682 | signals to 3D+t sequences of multi-spectral volumetric images, hence | |
683 | including 2D color images.") | |
684 | ;; Dual-licensed, either license applies. | |
685 | (license (list license:cecill license:cecill-c)))) | |
686 | ||
f23ba5d9 VM |
687 | (define-public gmic-qt |
688 | (package | |
689 | (inherit gmic) | |
690 | (name "gmic-qt") | |
691 | (arguments | |
692 | (substitute-keyword-arguments (package-arguments gmic) | |
693 | ((#:configure-flags _) | |
694 | `(list "-DGMIC_QT_HOST=none" "-DENABLE_DYNAMIC_LINKING=ON" | |
695 | (string-append "-DGMIC_LIB_PATH=" | |
696 | (assoc-ref %build-inputs "gmic") "/lib"))) | |
697 | ((#:phases phases) | |
698 | `(modify-phases ,phases | |
699 | (add-after 'unpack 'qt-chdir | |
700 | (lambda _ (chdir "gmic-qt") #t)))))) | |
701 | (native-inputs | |
702 | `(("pkg-config" ,pkg-config) | |
703 | ("qttools" ,qttools))) | |
704 | (inputs | |
705 | `(("gmic" ,gmic) | |
706 | ("qtbase" ,qtbase) | |
707 | ,@(package-inputs gmic))) | |
708 | (synopsis "Qt frontend for the G'MIC image processing framework") | |
709 | (license license:gpl3+))) | |
710 | ||
78e99ae6 VM |
711 | (define-public gmic-qt-krita |
712 | (package | |
713 | (inherit gmic-qt) | |
714 | (name "gmic-qt-krita") | |
715 | (arguments | |
716 | (substitute-keyword-arguments (package-arguments gmic-qt) | |
717 | ((#:configure-flags flags) | |
718 | '(list "-DGMIC_QT_HOST=krita" "-DENABLE_DYNAMIC_LINKING=ON" | |
719 | (string-append "-DGMIC_LIB_PATH=" | |
720 | (assoc-ref %build-inputs "gmic") "/lib"))))) | |
721 | (synopsis "Krita plugin for the G'MIC image processing framework"))) | |
722 | ||
e506b5e9 L |
723 | (define-public nip2 |
724 | (package | |
725 | (name "nip2") | |
f2d3d742 | 726 | (version "8.7.1") |
e506b5e9 L |
727 | (source |
728 | (origin | |
729 | (method url-fetch) | |
730 | (uri (string-append "https://github.com/libvips/nip2/releases/download/v" | |
731 | version "/nip2-" version ".tar.gz" )) | |
732 | (sha256 | |
f2d3d742 | 733 | (base32 "0l7n427njif53npqn02gfjjly8y3khbrkzqxp10j5vp9h97psgiw")))) |
e506b5e9 L |
734 | (build-system gnu-build-system) |
735 | (arguments | |
736 | `(#:phases | |
737 | (modify-phases %standard-phases | |
f2d3d742 | 738 | ;; test_conv.ws keep failing so disabling for now. |
e506b5e9 L |
739 | (add-after 'unpack 'disable-test-conv |
740 | (lambda _ | |
741 | (delete-file "test/workspaces/test_conv.ws") | |
742 | #t)) | |
743 | (add-before 'check 'set-home | |
744 | (lambda _ | |
745 | (setenv "HOME" "/tmp") #t))))) | |
746 | (inputs | |
747 | `(("vips" ,vips) | |
748 | ("glib" ,glib) | |
749 | ("libtiff" ,libtiff) | |
750 | ("gtk+-2" ,gtk+-2) | |
751 | ("libxml2" ,libxml2) | |
752 | ("libexif" ,libexif) | |
4bd428a7 | 753 | ("libjpeg" ,libjpeg-turbo) ;required by vips.pc |
e506b5e9 L |
754 | ("librsvg" ,librsvg) |
755 | ("fftw" ,fftw) | |
756 | ("libgsf" ,libgsf) | |
757 | ("imagemagick" ,imagemagick) | |
758 | ("orc" ,orc) | |
759 | ("matio" ,matio) | |
760 | ("lcms" ,lcms) | |
761 | ("libwebp" ,libwebp) | |
762 | ("openexr" ,openexr) | |
763 | ("poppler" ,poppler) | |
764 | ("gsl" ,gsl))) | |
765 | (native-inputs | |
766 | `(("flex" ,flex) | |
767 | ("bison" ,bison) | |
768 | ("pkg-config" ,pkg-config))) | |
769 | (home-page "https://github.com/libvips/nip2") | |
770 | (synopsis "Spreadsheet-like GUI for libvips") | |
771 | (description "This package provide a graphical user interface (GUI) for | |
772 | the VIPS image processing library. It's a little like a spreadsheet: you | |
773 | create a set of formula connecting your objects together, and on a change nip2 | |
774 | recalculates.") | |
775 | (license license:gpl2+))) | |
02e1acfb RW |
776 | |
777 | (define-public vxl | |
778 | (package | |
779 | (name "vxl") | |
780 | (version "2.0.2") | |
781 | (source | |
782 | (origin | |
783 | (method git-fetch) | |
784 | (uri (git-reference | |
b0e7b699 | 785 | (url "https://github.com/vxl/vxl") |
02e1acfb RW |
786 | (commit (string-append "v" version)))) |
787 | (file-name (git-file-name name version)) | |
788 | (sha256 | |
789 | (base32 "0949hw57szq8943f1whwqaz591xjmb19kj803hcv74hdai2b0ycg")) | |
790 | (modules '((guix build utils))) | |
791 | ;; TODO: vxl includes an old version of dcmtk. It won't build with | |
792 | ;; version 3.6.x. | |
793 | (snippet | |
794 | '(begin | |
795 | (for-each delete-file-recursively | |
796 | '("v3p/bzlib/" | |
797 | "v3p/geotiff/" | |
798 | "v3p/jpeg/" | |
799 | "v3p/png/" | |
800 | "v3p/tiff/" | |
801 | "v3p/zlib/")) | |
802 | (substitute* "v3p/CMakeLists.txt" | |
803 | (("add_subdirectory\\((tiff|png|jpeg|zlib|bzlib|geotiff)\\)") | |
804 | "")) | |
805 | #t)))) | |
806 | (build-system cmake-build-system) | |
807 | (inputs | |
808 | `(("libgeotiff" ,libgeotiff) | |
809 | ("libtiff" ,libtiff) | |
4bd428a7 | 810 | ("libjpeg" ,libjpeg-turbo) |
02e1acfb RW |
811 | ("libpng" ,libpng) |
812 | ("zlib" ,zlib))) | |
813 | (home-page "https://github.com/vxl/vxl/") | |
814 | (synopsis "Collection of C++ libraries for computer vision") | |
815 | (description "VXL (the Vision-something-Libraries) is a collection of C++ | |
816 | libraries designed for computer vision research and implementation.") | |
817 | (license license:bsd-3))) | |
4243af4e RW |
818 | |
819 | (define-public vxl-1 | |
820 | (package (inherit vxl) | |
821 | (name "vxl") | |
822 | (version "1.18.0") | |
823 | (source | |
824 | (origin | |
825 | (method git-fetch) | |
826 | (uri (git-reference | |
b0e7b699 | 827 | (url "https://github.com/vxl/vxl") |
4243af4e RW |
828 | (commit (string-append "v" version)))) |
829 | (file-name (git-file-name name version)) | |
830 | (sha256 | |
831 | (base32 "1g4mr2cc58jwm0vasscbd4y5380wj3ahkvq121z4gs83fhavvxgz")) | |
832 | (modules '((guix build utils))) | |
833 | (snippet | |
834 | '(begin | |
835 | (for-each delete-file-recursively | |
836 | '("v3p/bzlib/" | |
837 | "v3p/geotiff/" | |
838 | "v3p/png/" | |
839 | "v3p/tiff/" | |
840 | "v3p/zlib/")) | |
841 | (substitute* "v3p/CMakeLists.txt" | |
842 | (("add_subdirectory\\((tiff|png|jpeg|zlib|bzlib|geotiff)\\)") | |
843 | "")) | |
844 | #t)))) | |
845 | (arguments | |
846 | `(#:configure-flags | |
847 | ;; Needed for itk-snap | |
848 | (list "-DVNL_CONFIG_LEGACY_METHODS=ON"))))) | |
d7701e1b RW |
849 | |
850 | (define-public insight-toolkit | |
851 | (package | |
852 | (name "insight-toolkit") | |
853 | (version "5.0.0") | |
854 | (source | |
855 | (origin | |
856 | (method url-fetch) | |
857 | (uri (string-append "https://github.com/InsightSoftwareConsortium/ITK/" | |
858 | "releases/download/v" version "/InsightToolkit-" | |
859 | version ".tar.xz")) | |
860 | (sha256 | |
861 | (base32 "0bs63mk4q8jmx38f031jy5w5n9yy5ng9x8ijwinvjyvas8cichqi")))) | |
862 | (build-system cmake-build-system) | |
863 | (arguments | |
864 | `(#:tests? #f ; tests require network access and external data | |
865 | #:configure-flags | |
866 | '("-DITK_USE_GPU=ON" | |
867 | "-DITK_USE_SYSTEM_LIBRARIES=ON" | |
868 | "-DITK_USE_SYSTEM_GOOGLETEST=ON" | |
869 | "-DITK_BUILD_SHARED=ON" | |
870 | ;; This prevents "GTest::GTest" from being added to the ITK_LIBRARIES | |
871 | ;; variable in the installed CMake files. This is necessary as other | |
872 | ;; packages using insight-toolkit could not be configured otherwise. | |
873 | "-DGTEST_ROOT=gtest") | |
874 | #:phases | |
875 | (modify-phases %standard-phases | |
876 | (add-after 'unpack 'do-not-tune | |
877 | (lambda _ | |
878 | (substitute* "CMake/ITKSetStandardCompilerFlags.cmake" | |
879 | (("-mute=native") "")) | |
880 | #t))))) | |
881 | (inputs | |
882 | `(("eigen" ,eigen) | |
883 | ("expat" ,expat) | |
884 | ("fftw" ,fftw) | |
885 | ("fftwf" ,fftwf) | |
886 | ("hdf5" ,hdf5) | |
4bd428a7 | 887 | ("libjpeg" ,libjpeg-turbo) |
d7701e1b RW |
888 | ("libpng" ,libpng) |
889 | ("libtiff" ,libtiff) | |
890 | ("mesa" ,mesa-opencl) | |
891 | ("perl" ,perl) | |
892 | ("python" ,python) | |
893 | ("tbb" ,tbb) | |
894 | ("vxl" ,vxl-1) | |
895 | ("zlib" ,zlib))) | |
896 | (native-inputs | |
897 | `(("googletest" ,googletest) | |
898 | ("pkg-config" ,pkg-config))) | |
899 | (home-page "https://github.com/InsightSoftwareConsortium/ITK/") | |
900 | (synopsis "Scientific image processing, segmentation and registration") | |
901 | (description "The Insight Toolkit (ITK) is a toolkit for N-dimensional | |
902 | scientific image processing, segmentation, and registration. Segmentation is | |
903 | the process of identifying and classifying data found in a digitally sampled | |
904 | representation. Typically the sampled representation is an image acquired | |
905 | from such medical instrumentation as CT or MRI scanners. Registration is the | |
906 | task of aligning or developing correspondences between data. For example, in | |
907 | the medical environment, a CT scan may be aligned with a MRI scan in order to | |
908 | combine the information contained in both.") | |
909 | (license license:asl2.0))) | |
8f4d457d RW |
910 | |
911 | (define-public insight-toolkit-4 | |
912 | (package (inherit insight-toolkit) | |
913 | (version "4.13.2") | |
914 | (source | |
915 | (origin | |
916 | (method url-fetch) | |
917 | (uri (string-append "https://github.com/InsightSoftwareConsortium/ITK/" | |
918 | "releases/download/v" version "/InsightToolkit-" | |
919 | version ".tar.xz")) | |
920 | (sha256 | |
921 | (base32 "19cgfpd63gqrvc3m27m394gy2d7w79g5y6lvznb5qqr49lihbgns")))) | |
922 | (arguments | |
923 | `(#:tests? #f ; tests require network access and external data | |
924 | #:configure-flags | |
925 | '("-DITKV3_COMPATIBILITY=ON" ; needed for itk-snap | |
926 | "-DITK_USE_GPU=ON" | |
927 | "-DITK_USE_SYSTEM_LIBRARIES=ON" | |
928 | "-DITK_USE_SYSTEM_GOOGLETEST=ON" | |
929 | "-DITK_USE_SYSTEM_VXL=ON"))))) | |
07f36b0c RW |
930 | |
931 | (define-public insight-toolkit-4.12 | |
932 | (package (inherit insight-toolkit-4) | |
933 | (version "4.12.2") | |
934 | (source | |
935 | (origin | |
936 | (method url-fetch) | |
937 | (uri (string-append "mirror://sourceforge/itk/itk/4.12/" | |
938 | "InsightToolkit-" version ".tar.xz")) | |
939 | (sha256 | |
940 | (base32 "1qw9mxbh083siljygahl4gdfv91xvfd8hfl7ghwii19f60xrvn2w")))))) | |
1c4e6aa9 RW |
941 | |
942 | (define-public itk-snap | |
943 | (package | |
944 | (name "itk-snap") | |
945 | (version "3.8.0") | |
946 | (source | |
947 | (origin | |
948 | (method git-fetch) | |
949 | (uri (git-reference | |
950 | (url "https://git.code.sf.net/p/itk-snap/src") | |
951 | (commit (string-append "v" version)))) | |
952 | (file-name (git-file-name name version)) | |
953 | (sha256 | |
954 | (base32 "15i5ixpryfrbf3vrrb5rici8fb585f25k0v1ljds16bp1f1msr4q")))) | |
955 | (build-system cmake-build-system) | |
956 | (arguments | |
957 | `(#:configure-flags | |
958 | (list "-DSNAP_VERSION_GIT_SHA1=release" | |
959 | "-DSNAP_VERSION_GIT_BRANCH=release" | |
960 | "-DSNAP_VERSION_GIT_TIMESTAMP=0" | |
961 | "-DSNAP_PACKAGE_QT_PLUGINS=OFF" | |
0fe041bd | 962 | "-DCMAKE_POSITION_INDEPENDENT_CODE=ON") |
1c4e6aa9 RW |
963 | #:phases |
964 | (modify-phases %standard-phases | |
965 | ;; During the installation phase all libraries provided by all | |
966 | ;; dependencies will be copied to the lib directory. That's insane, | |
967 | ;; so we disable this. | |
968 | (add-after 'unpack 'do-not-copy-dependencies | |
969 | (lambda _ | |
970 | (substitute* "CMakeLists.txt" | |
971 | (("install_qt5_executable\ | |
972 | \\(\\$\\{SNAP_MAIN_INSTALL_DIR\\}/\\$\\{SNAP_EXE\\}\\)") | |
973 | "")) | |
974 | #t)) | |
975 | (add-after 'unpack 'disable-gui-tests | |
976 | (lambda _ | |
977 | ;; The GUI tests just time out. | |
978 | (substitute* "CMakeLists.txt" | |
979 | ((" (Workspace|DiffSpace|ProbeIntensity|RegionCompetition\ | |
980 | |RandomForest|RandomForestBailOut)") | |
981 | "")) | |
982 | #t)) | |
983 | (add-after 'unpack 'make-reproducible | |
984 | (lambda _ | |
985 | (substitute* "CMakeLists.txt" | |
986 | (("TODAY\\(SNAP_VERSION_COMPILE_DATE\\)") | |
987 | "SET(SNAP_VERSION_COMPILE_DATE \"(removed for reproducibility)\")")) | |
988 | #t)) | |
989 | (add-after 'unpack 'prepare-submodules | |
990 | (lambda* (#:key inputs #:allow-other-keys) | |
991 | (rmdir "Submodules/c3d") | |
992 | (copy-recursively (assoc-ref inputs "c3d-src") | |
993 | "Submodules/c3d") | |
994 | (substitute* '("Submodules/c3d/adapters/BiasFieldCorrectionN4.cxx" | |
995 | "Submodules/c3d/adapters/ApplyMetric.cxx") | |
996 | (("vcl_") "std::")) | |
997 | (rmdir "Submodules/greedy") | |
998 | (symlink (assoc-ref inputs "greedy-src") | |
999 | "Submodules/greedy") | |
1000 | #t)) | |
1001 | (add-after 'unpack 'fix-includes | |
1002 | (lambda _ | |
1003 | (substitute* "GUI/Model/RegistrationModel.cxx" | |
1004 | (("<vnl_symmetric_eigensystem.h>") | |
1005 | "<vnl/algo/vnl_symmetric_eigensystem.h>")) | |
1006 | #t)) | |
1007 | (add-before 'check 'prepare-tests | |
1008 | (lambda _ | |
1009 | ;; Needed by at least one test. | |
1010 | (setenv "HOME" "/tmp") | |
1011 | #t)) | |
1012 | (add-after 'install 'wrap-executable | |
1013 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
1014 | (let ((out (assoc-ref outputs "out"))) | |
1015 | (wrap-program (string-append out "/bin/itksnap") | |
1016 | `("QT_PLUGIN_PATH" ":" prefix | |
1017 | ,(map (lambda (label) | |
1018 | (string-append (assoc-ref inputs label) | |
1019 | "/lib/qt5/plugins")) | |
1020 | '("qtbase" "qtdeclarative")))) | |
1021 | #t)))))) | |
1022 | (inputs | |
1023 | `(("curl" ,curl) | |
1024 | ("fftw" ,fftw) | |
1025 | ("fftwf" ,fftwf) | |
1026 | ("glu" ,glu) | |
1027 | ("hdf5" ,hdf5) | |
1028 | ("mesa" ,mesa-opencl) | |
1029 | ;; This package does not build with either insight-toolkit 5.0.0 and | |
1030 | ;; not with 4.13. It really needs to be 4.12. | |
1031 | ("itk" ,insight-toolkit-4.12) | |
1032 | ("vtk" ,vtk-6) | |
1033 | ("qtbase" ,qtbase) | |
1034 | ("qtdeclarative" ,qtdeclarative) | |
1c4e6aa9 RW |
1035 | ("vxl" ,vxl-1) |
1036 | ("zlib" ,zlib))) | |
1037 | (native-inputs | |
1038 | `(("googletest" ,googletest) | |
957e0be3 | 1039 | ("qttools" ,qttools) |
1c4e6aa9 RW |
1040 | ("pkg-config" ,pkg-config) |
1041 | ("c3d-src" | |
1042 | ,(let* ((commit "f521358db26e00002c911cc47bf463b043942ad3") | |
1043 | (revision "1") | |
1044 | (version (git-version "0" revision commit))) | |
1045 | (origin | |
1046 | (method git-fetch) | |
1047 | (uri (git-reference | |
b0e7b699 | 1048 | (url "https://github.com/pyushkevich/c3d") |
1c4e6aa9 RW |
1049 | (commit commit))) |
1050 | (file-name (git-file-name "c3d" version)) | |
1051 | (sha256 | |
1052 | (base32 | |
1053 | "0kyv3rxrxwr8c3sa9zv01lsnhk95b27gx1s870k3yi8qp52h7bx3"))))) | |
1054 | ;; We are using an arbitrary commit from 2017 because the latest | |
1055 | ;; version breaks the build... | |
1056 | ("greedy-src" | |
1057 | ,(let* ((commit "97e340f7e8e66597599144947775e6039e79a0d3") | |
1058 | (revision "1") | |
1059 | (version (git-version "0" revision commit))) | |
1060 | (origin | |
1061 | (method git-fetch) | |
1062 | (uri (git-reference | |
b0e7b699 | 1063 | (url "https://github.com/pyushkevich/greedy") |
1c4e6aa9 RW |
1064 | (commit commit))) |
1065 | (file-name (git-file-name "greedy" version)) | |
1066 | (sha256 | |
1067 | (base32 | |
1068 | "0k5bc9za4jrc8z9dj08z1rkcp5xf0gnd1d2jmi1w9ny4vxh2q2ab"))))))) | |
1069 | (home-page "https://sourceforge.net/p/itk-snap/") | |
1070 | (synopsis "Medical image segmentation") | |
1071 | (description "ITK-SNAP is a tool for segmenting anatomical structures in | |
1072 | medical images. It provides an automatic active contour segmentation | |
1073 | pipeline, along with supporting a manual segmentation toolbox. ITK-SNAP has a | |
1074 | full-featured UI aimed at clinical researchers.") | |
1075 | ;; This includes the submodules greedy and c3d. | |
1076 | (license license:gpl3+))) | |
85c4f486 PN |
1077 | |
1078 | (define-public metapixel | |
1079 | ;; Follow stable branch. | |
1080 | (let ((commit "98ee9daa093b6c334941242e63f90b1c2876eb4f")) | |
1081 | (package | |
1082 | (name "metapixel") | |
1083 | (version (git-version "1.0.2" "1" commit)) | |
1084 | (source | |
1085 | (origin | |
1086 | (method git-fetch) | |
1087 | (uri (git-reference | |
1088 | (url "https://github.com/schani/metapixel") | |
1089 | (commit commit) | |
1090 | ;; TODO: Package rwimg and lispreader? | |
1091 | (recursive? #t))) | |
1092 | (file-name (git-file-name name version)) | |
1093 | (sha256 | |
1094 | (base32 "0r7n3a6bvcxkbpda4mwmrpicii09iql5z69nkjqygkwxw7ny3309")))) | |
1095 | (build-system gnu-build-system) | |
1096 | (inputs | |
1097 | `(("giflib" ,giflib) | |
1098 | ("libjpeg" ,libjpeg-turbo) | |
1099 | ("libpng" ,libpng) | |
1100 | ("perl" ,perl))) | |
1101 | (native-inputs | |
1102 | `(("pkg-config" ,pkg-config) | |
1103 | ("docbook-xml" ,docbook-xml) | |
1104 | ("docbook-xsl" ,docbook-xsl) | |
1105 | ("xsltproc" ,libxslt))) | |
1106 | (arguments | |
1107 | `(#:tests? #f ; No tests. | |
1108 | #:make-flags (list | |
1109 | (string-append "PREFIX=" (assoc-ref %outputs "out")) | |
1110 | (string-append "MANPAGE_XSL=" | |
1111 | (assoc-ref %build-inputs "docbook-xsl") | |
1112 | "/xml/xsl/docbook-xsl-*/manpages/docbook.xsl")) | |
1113 | #:phases | |
1114 | (modify-phases %standard-phases | |
1115 | (delete 'configure) | |
1116 | (add-before 'install 'make-local-docbook-xml | |
1117 | (lambda* (#:key inputs #:allow-other-keys) | |
1118 | (substitute* "metapixel.xml" | |
1119 | (("http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd") | |
1120 | (string-append (assoc-ref inputs "docbook-xml") | |
1121 | "/xml/dtd/docbook/docbookx.dtd"))) | |
1122 | #t)) | |
1123 | (add-before 'install 'fix-directory-creation | |
1124 | (lambda* (#:key outputs #:allow-other-keys) | |
1125 | (mkdir-p (string-append (assoc-ref outputs "out") "/share/man/man1")) | |
1126 | #t))))) | |
1127 | (home-page "https://www.complang.tuwien.ac.at/schani/metapixel/") | |
1128 | (synopsis "Photomosaics generator") | |
1129 | (description "Metapixel is a program for generating photomosaics. It can | |
1130 | generate classical photomosaics, in which the source image is viewed as a | |
1131 | matrix of equally sized rectangles for each of which a matching image is | |
1b8be80e | 1132 | substituted, as well as collage-style photomosaics, in which rectangular parts |
85c4f486 PN |
1133 | of the source image at arbitrary positions (i.e. not aligned to a matrix) are |
1134 | substituted by matching images.") | |
1135 | (license license:gpl2)))) | |
a76e9d13 BT |
1136 | |
1137 | (define-public scantailor-advanced | |
1138 | (let ((commit "3d1e74e6ace413733511086934a66f4e3f7a6027")) | |
1139 | (package | |
1140 | (name "scantailor-advanced") | |
1141 | (version (string-append "1.0.16-" (string-take commit 7))) | |
1142 | (source | |
1143 | (origin | |
1144 | (method git-fetch) | |
1145 | (uri (git-reference | |
1146 | (url "https://github.com/4lex4/scantailor-advanced") | |
1147 | (commit commit))) | |
1148 | (file-name (git-file-name name version)) | |
1149 | (sha256 | |
1150 | (base32 | |
1151 | "0kixwjb2x457dq7927hkh34c803p7yh1pmn6n61rk9shqrcg492h")))) | |
1152 | (build-system qt-build-system) | |
1153 | (native-inputs | |
1154 | `(("qttools" ,qttools))) | |
1155 | (inputs | |
1156 | `(("boost" ,boost) | |
1157 | ("libjpeg" ,libjpeg-turbo) | |
1158 | ("libpng" ,libpng) | |
1159 | ("libtiff" ,libtiff) | |
1160 | ("qtbase" ,qtbase) | |
1161 | ("qtsvg" ,qtsvg) | |
1162 | ("zlib" ,zlib))) | |
1163 | (arguments | |
1164 | `(#:phases | |
1165 | (modify-phases %standard-phases | |
1166 | ;; Some tests require a display and fail with offscreen mode. | |
1167 | (add-after 'unpack 'disable-failing-tests | |
1168 | (lambda _ | |
1169 | (setenv "ARGS" "--exclude-regex \"imageproc_.*\"") | |
1170 | #t))))) | |
1171 | (home-page "https://github.com/4lex4/scantailor-advanced") | |
1172 | (synopsis "Clean up scanned pages") | |
1173 | (description "Scan Tailor is an interactive post-processing tool for | |
1174 | scanned pages. It performs operations such as page splitting, deskewing, | |
1175 | adding/removing borders, and others. You give it raw scans, and you get pages | |
1176 | ready to be printed or assembled into a PDF or DJVU file. Scanning, optical | |
1177 | character recognition, and assembling multi-page documents are out of scope of | |
1178 | this project. | |
1179 | ||
1180 | Scan Tailer Advanced is a fork of Scan Tailer that merges Scan Tailor Featured | |
1181 | and Scan Tailor Enhanced versions as well as including many more bug fixes.") | |
1182 | (license license:gpl3+)))) | |
58a5746e OM |
1183 | |
1184 | (define-public stiff | |
1185 | (package | |
1186 | (name "stiff") | |
1187 | (version "2.4.0") | |
1188 | (source | |
1189 | (origin | |
1190 | (method url-fetch) | |
1191 | (uri (string-append "https://www.astromatic.net/download/stiff/stiff-" | |
1192 | version ".tar.gz")) | |
1193 | (sha256 | |
1194 | (base32 "14m92dskzw7bwsr64ha4p0mj3ndv13gwcbfic3qxrs3zq5353s7l")))) | |
1195 | (build-system gnu-build-system) | |
1196 | (inputs | |
1197 | `(("libtiff" ,libtiff) | |
1198 | ("zlib" ,zlib) | |
1199 | ("libjpeg-turbo" ,libjpeg-turbo))) | |
1200 | (home-page "https://www.astromatic.net/software/stiff") | |
1201 | (synopsis "Convert scientific FITS images to TIFF format") | |
1202 | (description | |
1203 | "STIFF is a program that converts scientific @acronym{FITS, Flexible Image | |
1204 | Transport System} images to the more popular TIFF format for illustration | |
1205 | purposes.") | |
1206 | (license license:gpl3+))) |