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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> |
d769fcd6 | 19 | ;;; Copyright © 2021 Paul Garlick <pgarlick@tourbillion-technology.com> |
504c285d JD |
20 | ;;; |
21 | ;;; This file is part of GNU Guix. | |
22 | ;;; | |
23 | ;;; GNU Guix is free software; you can redistribute it and/or modify it | |
24 | ;;; under the terms of the GNU General Public License as published by | |
25 | ;;; the Free Software Foundation; either version 3 of the License, or (at | |
26 | ;;; your option) any later version. | |
27 | ;;; | |
28 | ;;; GNU Guix is distributed in the hope that it will be useful, but | |
29 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of | |
30 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
31 | ;;; GNU General Public License for more details. | |
32 | ;;; | |
33 | ;;; You should have received a copy of the GNU General Public License | |
34 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. | |
35 | ||
36 | (define-module (gnu packages image-processing) | |
37 | #:use-module ((guix licenses) #:prefix license:) | |
38 | #:use-module (guix packages) | |
39 | #:use-module (guix utils) | |
40 | #:use-module (guix download) | |
6c56e9c4 | 41 | #:use-module (guix git-download) |
a76e9d13 | 42 | #:use-module (guix build-system qt) |
cdb2a211 | 43 | #:use-module (guix build-system cmake) |
504c285d JD |
44 | #:use-module (guix build-system gnu) |
45 | #:use-module (gnu packages) | |
cdb2a211 | 46 | #:use-module (gnu packages algebra) |
e506b5e9 | 47 | #:use-module (gnu packages bison) |
cdb2a211 | 48 | #:use-module (gnu packages boost) |
d7701e1b | 49 | #:use-module (gnu packages check) |
504c285d | 50 | #:use-module (gnu packages compression) |
1c4e6aa9 | 51 | #:use-module (gnu packages curl) |
85c4f486 | 52 | #:use-module (gnu packages docbook) |
504c285d | 53 | #:use-module (gnu packages documentation) |
e506b5e9 | 54 | #:use-module (gnu packages flex) |
fb226b43 | 55 | #:use-module (gnu packages fontutils) |
02e1acfb | 56 | #:use-module (gnu packages geo) |
5bbd6931 | 57 | #:use-module (gnu packages ghostscript) |
fb226b43 | 58 | #:use-module (gnu packages gl) |
5bbd6931 | 59 | #:use-module (gnu packages glib) |
cdb2a211 JD |
60 | #:use-module (gnu packages gnome) |
61 | #:use-module (gnu packages graphics) | |
62 | #:use-module (gnu packages graphviz) | |
5bbd6931 | 63 | #:use-module (gnu packages gstreamer) |
62834314 | 64 | #:use-module (gnu packages gtk) |
5d0f394b | 65 | #:use-module (gnu packages icu4c) |
504c285d | 66 | #:use-module (gnu packages image) |
5bbd6931 | 67 | #:use-module (gnu packages imagemagick) |
cdb2a211 | 68 | #:use-module (gnu packages maths) |
5bbd6931 | 69 | #:use-module (gnu packages pdf) |
cdb2a211 | 70 | #:use-module (gnu packages perl) |
62834314 | 71 | #:use-module (gnu packages photo) |
cdb2a211 | 72 | #:use-module (gnu packages pkg-config) |
62834314 | 73 | #:use-module (gnu packages protobuf) |
cdb2a211 | 74 | #:use-module (gnu packages python) |
44d10b1f | 75 | #:use-module (gnu packages python-xyz) |
1c4e6aa9 | 76 | #:use-module (gnu packages qt) |
fb226b43 | 77 | #:use-module (gnu packages serialization) |
a675c01f | 78 | #:use-module (gnu packages sqlite) |
d7701e1b | 79 | #:use-module (gnu packages tbb) |
8486a80d | 80 | #:use-module (gnu packages tls) |
2283cf4c | 81 | #:use-module (gnu packages version-control) |
62834314 | 82 | #:use-module (gnu packages video) |
fb226b43 | 83 | #:use-module (gnu packages xiph) |
cdb2a211 | 84 | #:use-module (gnu packages xml) |
ebe0271a | 85 | #:use-module (gnu packages xorg) |
18696f7a RW |
86 | #:use-module (ice-9 match) |
87 | #:use-module (srfi srfi-1)) | |
504c285d | 88 | |
504c285d JD |
89 | (define-public dcmtk |
90 | (package | |
91 | (name "dcmtk") | |
5d0f394b | 92 | (version "3.6.6") |
882d579d TGR |
93 | (source |
94 | (origin | |
95 | (method url-fetch) | |
96 | (uri | |
97 | (string-append "ftp://dicom.offis.de/pub/dicom/offis/software/dcmtk/" | |
98 | "dcmtk" (string-join (string-split version #\.) "") | |
99 | "/dcmtk-" version ".tar.gz")) | |
100 | (sha256 | |
5d0f394b | 101 | (base32 "13j5yf3p6qj3mr17d77r3kcqchf055hgvk1w15vmdr8f54mwcnb8")))) |
882d579d | 102 | (build-system cmake-build-system) |
504c285d | 103 | (inputs |
5d0f394b | 104 | `(("icu4c" ,icu4c) |
4bd428a7 | 105 | ("libjpeg" ,libjpeg-turbo) |
504c285d | 106 | ("libpng" ,libpng) |
882d579d | 107 | ("libtiff" ,libtiff) |
8486a80d TGR |
108 | ("libxml2" ,libxml2) |
109 | ("openssl" ,openssl) | |
504c285d JD |
110 | ("zlib" ,zlib))) |
111 | (native-inputs | |
882d579d | 112 | `(("doxygen" ,doxygen))) ; for HTML documentation |
d2ad4f2e | 113 | (home-page "https://dcmtk.org") |
504c285d JD |
114 | (synopsis "Libraries and programs implementing parts of the DICOM standard") |
115 | (description "DCMTK is a collection of libraries and applications | |
116 | implementing large parts the DICOM standard. It includes software for | |
117 | examining, constructing and converting DICOM image files, handling offline | |
118 | media, sending and receiving images over a network connection, as well as | |
119 | demonstrative image storage and worklist servers.") | |
120 | (license (license:fsf-free | |
121 | "file://COPYRIGHT" | |
122 | "A union of the Apache 2.0 licence and various non-copyleft | |
123 | licences similar to the Modified BSD licence.")))) | |
cdb2a211 JD |
124 | |
125 | (define-public mia | |
126 | (package | |
127 | (name "mia") | |
11861d2b | 128 | (version "2.4.6") |
cdb2a211 JD |
129 | (source (origin |
130 | (method url-fetch) | |
131 | (uri (string-append "mirror://sourceforge/mia/mia/" | |
132 | (version-major+minor version) | |
133 | "/mia-" version ".tar.xz")) | |
134 | (sha256 | |
135 | (base32 | |
11861d2b | 136 | "0j4nd5z7i3v199jh7hqqhwd4g7snchizkc7rhzanpvngqg91m1pb")))) |
cdb2a211 JD |
137 | (build-system cmake-build-system) |
138 | (arguments | |
139 | `(#:configure-flags | |
140 | (list "-DMIA_CREATE_NIPYPE_INTERFACES=0" | |
cdb2a211 JD |
141 | "-DCMAKE_CXX_FLAGS=-fpermissive"))) |
142 | (inputs | |
143 | `(("boost" ,boost) | |
144 | ("dcmtk" ,dcmtk) | |
145 | ("doxygen" ,doxygen) | |
146 | ("eigen" ,eigen) | |
147 | ("fftw" ,fftw) | |
148 | ("fftwf" ,fftwf) | |
149 | ("gsl" ,gsl) | |
150 | ("gts" ,gts) | |
151 | ("hdf5" ,hdf5) | |
152 | ("itpp" ,itpp) | |
4bd428a7 | 153 | ("libjpeg" ,libjpeg-turbo) |
cdb2a211 JD |
154 | ("libpng" ,libpng) |
155 | ("libtiff" ,libtiff) | |
156 | ("libxml" ,libxml2) | |
157 | ("libxml++" ,libxml++) | |
158 | ("maxflow" ,maxflow) | |
159 | ("niftilib" ,niftilib) | |
160 | ("nlopt" ,nlopt) | |
161 | ("openexr" ,openexr) | |
162 | ("python-lxml" ,python2-lxml) | |
163 | ("vtk" ,vtk))) | |
164 | (native-inputs | |
165 | `(("pkg-config" ,pkg-config) | |
166 | ("python" ,python-2))) | |
167 | (home-page "http://mia.sourceforge.net") | |
168 | (synopsis "Toolkit for gray scale medical image analysis") | |
169 | (description "MIA provides a combination of command line tools, plug-ins, | |
170 | and libraries that make it possible run image processing tasks interactively | |
171 | in a command shell and to prototype using the shell's scripting language. It | |
172 | is built around a plug-in structure that makes it easy to add functionality | |
173 | without compromising the original code base and it makes use of a wide variety | |
174 | of external libraries that provide additional functionality.") | |
175 | (license license:gpl3+))) | |
fb226b43 | 176 | |
2283cf4c TGR |
177 | (define-public opencolorio |
178 | (package | |
179 | (name "opencolorio") | |
180 | (version "1.1.1") | |
181 | (source | |
182 | (origin | |
183 | (method git-fetch) | |
184 | (uri (git-reference | |
185 | (url "https://github.com/AcademySoftwareFoundation/OpenColorIO") | |
186 | (commit (string-append "v" version)))) | |
187 | (sha256 | |
188 | (base32 "12srvxca51czpfjl0gabpidj9n84mw78ivxy5w75qhq2mmc798sb")) | |
189 | (file-name (git-file-name name version)) | |
190 | (modules '((guix build utils))) | |
191 | (snippet | |
192 | `(begin | |
193 | ;; Remove bundled tarballs, patches, and .jars(!). XXX: Upstream | |
194 | ;; claims to have fixed USE_EXTERNAL_YAML, but it still fails with: | |
195 | ;; https://github.com/AcademySoftwareFoundation/OpenColorIO/issues/517 | |
196 | ;; When removing it, also remove it from the licence field comment. | |
197 | (for-each delete-file-recursively | |
198 | (filter | |
199 | (lambda (full-name) | |
200 | (let ((file (basename full-name))) | |
201 | (not (or (string-prefix? "yaml-cpp-0.3" file) | |
202 | (string=? "unittest.h" file))))) | |
203 | (find-files "ext" ".*"))) | |
204 | ||
205 | #t)))) | |
206 | (build-system cmake-build-system) | |
207 | (arguments | |
208 | `(#:configure-flags | |
209 | (list (string-append "-DCMAKE_CXX_FLAGS=" | |
210 | "-Wno-error=deprecated-declarations " | |
211 | "-Wno-error=unused-function") | |
212 | "-DOCIO_BUILD_STATIC=OFF" | |
213 | ;; "-DUSE_EXTERNAL_YAML=ON" | |
214 | "-DUSE_EXTERNAL_TINYXML=ON" | |
215 | "-DUSE_EXTERNAL_LCMS=ON") | |
216 | #:phases | |
217 | (modify-phases %standard-phases | |
218 | (add-after 'unpack 'patch-test-suite | |
219 | (lambda _ | |
220 | (substitute* "src/core_tests/CMakeLists.txt" | |
221 | (("/bin/sh") (which "bash"))) | |
222 | #t))))) | |
223 | (native-inputs | |
224 | `(("git" ,git) | |
225 | ("pkg-config" ,pkg-config))) | |
226 | (inputs | |
227 | ;; XXX Adding freeglut, glew, ilmbase, mesa, and openimageio for | |
228 | ;; ocioconvert fails: error: conflicting declaration ?typedef void | |
229 | ;; (* PFNGLGETFRAGMENTMATERIALFVSGIXPROC)(GLenum, GLenum, GLfloat*) | |
230 | `(("lcms" ,lcms) | |
231 | ("openexr" ,openexr) | |
232 | ("tinyxml" ,tinyxml))) | |
233 | (home-page "https://opencolorio.org") | |
234 | (synopsis "Color management for visual effects and animation") | |
235 | (description | |
236 | "OpenColorIO, or OCIO, is a complete color management solution geared | |
237 | towards motion picture production, with an emphasis on visual effects and | |
238 | computer animation. It provides a straightforward and consistent user | |
239 | experience across all supporting applications while allowing for sophisticated | |
240 | back-end configuration options suitable for high-end production usage. | |
241 | ||
242 | OCIO is compatible with the @acronym{ACES, Academy Color Encoding | |
243 | Specification} and is @acronym{LUT, look-up table}-format agnostic, supporting | |
244 | many popular formats.") | |
245 | (license (list license:expat ; docs/ociotheme/static, ext/yaml-cpp-* | |
246 | license:zlib ; src/core/md5 | |
247 | license:bsd-3)))) ; the rest | |
248 | ||
fb226b43 JD |
249 | (define-public vtk |
250 | (package | |
251 | (name "vtk") | |
48f7aa1c | 252 | (version "9.0.1") |
fb226b43 JD |
253 | (source (origin |
254 | (method url-fetch) | |
f1d4f264 | 255 | (uri (string-append "https://vtk.org/files/release/" |
fb226b43 JD |
256 | (version-major+minor version) |
257 | "/VTK-" version ".tar.gz")) | |
258 | (sha256 | |
259 | (base32 | |
48f7aa1c | 260 | "1ir2lq9i45ls374lcmjzw0nrm5l5hnm1w47lg8g8d0n2j7hsaf8v")) |
251b0f7a FG |
261 | (patches |
262 | (search-patches "vtk-fix-freetypetools-build-failure.patch")) | |
b17b5411 EF |
263 | (modules '((guix build utils))) |
264 | (snippet | |
265 | '(begin | |
266 | (for-each | |
267 | (lambda (dir) | |
268 | (delete-file-recursively | |
269 | (string-append "ThirdParty/" dir "/vtk" dir))) | |
48f7aa1c | 270 | ;; pugixml depended upon unconditionally |
a675c01f EF |
271 | '("doubleconversion" "eigen" "expat" "freetype" "gl2ps" |
272 | "glew" "hdf5" "jpeg" "jsoncpp" "libproj" "libxml2" "lz4" | |
48f7aa1c | 273 | "netcdf" "ogg" "png" "sqlite" "theora" "tiff" "zlib")) |
b17b5411 | 274 | #t)))) |
e025de68 | 275 | (properties `((release-monitoring-url . "https://vtk.org/download/"))) |
fb226b43 JD |
276 | (build-system cmake-build-system) |
277 | (arguments | |
278 | '(#:build-type "Release" ;Build without '-g' to save space. | |
a675c01f | 279 | #:configure-flags '(;"-DBUILD_TESTING:BOOL=TRUE" |
48f7aa1c AT |
280 | ; ; not honored |
281 | "-DVTK_USE_EXTERNAL=OFF" ;; default | |
282 | "-DVTK_MODULE_USE_EXTERNAL_VTK_doubleconversion=ON" | |
283 | "-DVTK_MODULE_USE_EXTERNAL_VTK_eigen=ON" | |
284 | "-DVTK_MODULE_USE_EXTERNAL_VTK_expat=ON" | |
285 | "-DVTK_MODULE_USE_EXTERNAL_VTK_freetype=ON" | |
286 | "-DVTK_MODULE_USE_EXTERNAL_VTK_gl2ps=ON" | |
287 | "-DVTK_MODULE_USE_EXTERNAL_VTK_glew=ON" | |
288 | "-DVTK_MODULE_USE_EXTERNAL_VTK_hdf5=ON" | |
289 | "-DVTK_MODULE_USE_EXTERNAL_VTK_jpeg=ON" | |
290 | "-DVTK_MODULE_USE_EXTERNAL_VTK_jsoncpp=ON" | |
291 | "-DVTK_MODULE_USE_EXTERNAL_VTK_libproj=ON" | |
292 | "-DVTK_MODULE_USE_EXTERNAL_VTK_libxml2=ON" | |
293 | "-DVTK_MODULE_USE_EXTERNAL_VTK_lz4=ON" | |
294 | "-DVTK_MODULE_USE_EXTERNAL_VTK_netcdf=ON" | |
295 | "-DVTK_MODULE_USE_EXTERNAL_VTK_ogg=ON" | |
296 | "-DVTK_MODULE_USE_EXTERNAL_VTK_png=ON" | |
297 | ;"-DVTK_MODULE_USE_EXTERNAL_VTK_pugixml=ON" ; breaks IO/CityGML | |
298 | "-DVTK_MODULE_USE_EXTERNAL_VTK_sqlite=ON" | |
299 | "-DVTK_MODULE_USE_EXTERNAL_VTK_theora=ON" | |
300 | "-DVTK_MODULE_USE_EXTERNAL_VTK_tiff=ON" | |
301 | "-DVTK_MODULE_USE_EXTERNAL_VTK_zlib=ON" | |
d769fcd6 PG |
302 | "-DVTK_WRAP_PYTHON=ON" |
303 | "-DVTK_PYTHON_VERSION:STRING=3" | |
48f7aa1c AT |
304 | ) |
305 | #:phases | |
306 | (modify-phases %standard-phases | |
307 | (add-after 'unpack 'patch-sources | |
308 | (lambda _ | |
309 | (substitute* "Common/Core/vtkFloatingPointExceptions.cxx" | |
310 | (("<fenv.h>") "<cfenv>")) | |
311 | (substitute* "Common/Core/CMakeLists.txt" | |
312 | (("fenv.h") "cfenv"))))) | |
a675c01f | 313 | #:tests? #f)) ;XXX: test data not included |
fb226b43 | 314 | (inputs |
a675c01f EF |
315 | `(("double-conversion" ,double-conversion) |
316 | ("eigen" ,eigen) | |
317 | ("expat" ,expat) | |
fb226b43 | 318 | ("freetype" ,freetype) |
a675c01f EF |
319 | ("gl2ps" ,gl2ps) |
320 | ("glew" ,glew) | |
fac4e4ae | 321 | ("glu" ,glu) |
fb226b43 | 322 | ("hdf5" ,hdf5) |
4bd428a7 | 323 | ("jpeg" ,libjpeg-turbo) |
fb226b43 | 324 | ("jsoncpp" ,jsoncpp) |
fb226b43 | 325 | ("libtheora" ,libtheora) |
fac4e4ae EF |
326 | ("libX11" ,libx11) |
327 | ("libxml2" ,libxml2) | |
328 | ("libXt" ,libxt) | |
a675c01f | 329 | ("lz4" ,lz4) |
fac4e4ae | 330 | ("mesa" ,mesa) |
a675c01f | 331 | ("netcdf" ,netcdf) |
fb226b43 | 332 | ("png" ,libpng) |
a675c01f | 333 | ("proj" ,proj.4) |
d769fcd6 | 334 | ("python", python) |
a675c01f EF |
335 | ;("pugixml" ,pugixml) |
336 | ("sqlite" ,sqlite) | |
fb226b43 | 337 | ("tiff" ,libtiff) |
fac4e4ae | 338 | ("xorgproto" ,xorgproto) |
fb226b43 | 339 | ("zlib" ,zlib))) |
48f7aa1c AT |
340 | (propagated-inputs |
341 | ;; VTK's 'VTK-vtk-module-find-packages.cmake' calls | |
342 | ;; 'find_package(THEORA)', which in turns looks for libogg. | |
343 | `(("libogg" ,libogg))) | |
f1d4f264 | 344 | (home-page "https://vtk.org/") |
fb226b43 JD |
345 | (synopsis "Libraries for 3D computer graphics") |
346 | (description | |
347 | "The Visualization Toolkit (VTK) is a C++ library for 3D computer graphics, | |
348 | image processing and visualization. It supports a wide variety of | |
349 | visualization algorithms including: scalar, vector, tensor, texture, and | |
350 | volumetric methods; and advanced modeling techniques such as: implicit | |
351 | modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay | |
352 | triangulation. VTK has an extensive information visualization framework, has | |
353 | a suite of 3D interaction widgets, supports parallel processing, and | |
354 | integrates with various databases on GUI toolkits such as Qt and Tk.") | |
355 | (license license:bsd-3))) | |
62834314 | 356 | |
950475bb EZ |
357 | ;; freecad needs an old version of VTK, because VTK's API changed from 8 to 9 |
358 | (define-public vtk-8 | |
359 | (package (inherit vtk) | |
360 | (version "8.2.0") | |
361 | (source (origin | |
362 | (method url-fetch) | |
363 | (uri (string-append "https://vtk.org/files/release/" | |
364 | (version-major+minor version) | |
365 | "/VTK-" version ".tar.gz")) | |
366 | (sha256 | |
367 | (base32 | |
368 | "1fspgp8k0myr6p2a6wkc21ldcswb4bvmb484m12mxgk1a9vxrhrl")))) | |
369 | (inputs | |
370 | `(("jsoncpp" ,jsoncpp-for-tensorflow) | |
371 | ,@(alist-delete "jsoncpp" (package-inputs vtk)))))) | |
372 | ||
18696f7a RW |
373 | ;; itksnap needs an older variant of VTK. |
374 | (define-public vtk-6 | |
375 | (package (inherit vtk) | |
376 | (version "6.3.0") | |
377 | (source (origin | |
378 | (method url-fetch) | |
379 | (uri (string-append "https://vtk.org/files/release/" | |
380 | (version-major+minor version) | |
381 | "/VTK-" version ".tar.gz")) | |
382 | (sha256 | |
383 | (base32 | |
384 | "0pla1r5mvkgl4sl213gfdhzrypdgai0h3z5mfgm6p9jz9hsr794j")))) | |
385 | (inputs | |
386 | `(("jsoncpp" ,jsoncpp-for-tensorflow) | |
387 | ,@(alist-delete "jsoncpp" (package-inputs vtk)))))) | |
388 | ||
62834314 BH |
389 | (define-public opencv |
390 | (package | |
391 | (name "opencv") | |
63856931 | 392 | (version "3.4.3") |
62834314 | 393 | (source (origin |
6c56e9c4 EF |
394 | (method git-fetch) |
395 | (uri (git-reference | |
396 | (url "https://github.com/opencv/opencv") | |
397 | (commit version))) | |
398 | (file-name (git-file-name name version)) | |
62834314 BH |
399 | (sha256 |
400 | (base32 | |
6c56e9c4 | 401 | "06bc61r8myym4s8im10brdjfg4wxkrvsbhhl7vr1msdan2xddzi3")) |
8bf70426 TGR |
402 | (patches |
403 | (search-patches "opencv-fix-build-of-grfmt_jpeg2000.cpp.patch")) | |
62834314 BH |
404 | (modules '((guix build utils))) |
405 | (snippet | |
406 | '(begin | |
407 | ;; Remove external libraries. We have all available in Guix: | |
408 | (delete-file-recursively "3rdparty") | |
409 | ||
410 | ;; Milky icon set is non-free: | |
411 | (delete-file-recursively "modules/highgui/src/files_Qt/Milky") | |
412 | ||
413 | ;; Some jars found: | |
414 | (for-each delete-file | |
415 | '("modules/java/test/pure_test/lib/junit-4.11.jar" | |
6c56e9c4 EF |
416 | "samples/java/sbt/sbt/sbt-launch.jar")) |
417 | #t)))) | |
62834314 BH |
418 | (build-system cmake-build-system) |
419 | (arguments | |
420 | `(#:configure-flags | |
421 | (list "-DWITH_IPP=OFF" | |
422 | "-DWITH_ITT=OFF" | |
6949f45c | 423 | "-DWITH_CAROTENE=OFF" ; only visible on arm/aarch64 |
fdeb2def | 424 | "-DENABLE_PRECOMPILED_HEADERS=OFF" |
62834314 BH |
425 | |
426 | ;; CPU-Features: | |
427 | ;; See cmake/OpenCVCompilerOptimizations.cmake | |
428 | ;; (CPU_ALL_OPTIMIZATIONS) for a list of all optimizations | |
429 | ;; BASELINE is the minimum optimization all CPUs must support | |
430 | ;; | |
ebe0271a EF |
431 | ;; DISPATCH is the list of optional dispatches. |
432 | "-DCPU_BASELINE=SSE2" | |
62834314 | 433 | |
ebe0271a EF |
434 | ,@(match (%current-system) |
435 | ("x86_64-linux" | |
436 | '("-DCPU_DISPATCH=NEON;VFPV3;FP16;SSE;SSE2;SSE3;SSSE3;SSE4_1;SSE4_2;POPCNT;AVX;FP16;AVX2;FMA3;AVX_512F;AVX512_SKX" | |
437 | "-DCPU_DISPATCH_REQUIRE=SSE3,SSSE3,SSE4_1,SSE4_2,AVX,AVX2")) | |
438 | ("armhf-linux" | |
439 | '("-DCPU_BASELINE_DISABLE=NEON")) ; causes build failures | |
440 | ("aarch64-linux" | |
441 | '("-DCPU_BASELINE=NEON" | |
442 | "-DCPU_DISPATCH=NEON;VFPV3;FP16")) | |
443 | (_ '())) | |
62834314 BH |
444 | |
445 | "-DBUILD_PERF_TESTS=OFF" | |
6949f45c | 446 | "-DBUILD_TESTS=ON" |
62834314 | 447 | |
b5baf952 | 448 | (string-append "-DOPENCV_EXTRA_MODULES_PATH=" (getcwd) |
6c56e9c4 | 449 | "/opencv-contrib/modules") |
62834314 BH |
450 | |
451 | ;;Define test data: | |
b5baf952 | 452 | (string-append "-DOPENCV_TEST_DATA_PATH=" (getcwd) |
6c56e9c4 | 453 | "/opencv-extra/testdata") |
62834314 BH |
454 | |
455 | ;; Is ON by default and would try to rebuild 3rd-party protobuf, | |
456 | ;; which we had removed, which would lead to an error: | |
457 | "-DBUILD_PROTOBUF=OFF" | |
458 | ||
459 | ;; Rebuild protobuf files, because we have a slightly different | |
460 | ;; version than the included one. If we would not update, we | |
461 | ;; would get a compile error later: | |
462 | "-DPROTOBUF_UPDATE_FILES=ON" | |
463 | ||
464 | ;; xfeatures2d disabled, because it downloads extra binaries from | |
465 | ;; https://github.com/opencv/opencv_3rdparty | |
466 | ;; defined in xfeatures2d/cmake/download_{vgg|bootdesc}.cmake | |
467 | ;; Cmp this bug entry: | |
468 | ;; https://github.com/opencv/opencv_contrib/issues/1131 | |
469 | "-DBUILD_opencv_xfeatures2d=OFF") | |
470 | #:phases | |
471 | (modify-phases %standard-phases | |
472 | (add-after 'unpack 'disable-broken-tests | |
473 | (lambda _ | |
474 | ;; These tests fails with: | |
475 | ;; vtkXOpenGLRenderWindow (0x723990): Could not find a decent config | |
476 | ;; I think we have no OpenGL support with the Xvfb. | |
477 | (substitute* '("modules/viz/test/test_tutorial3.cpp" | |
478 | "modules/viz/test/test_main.cpp" | |
479 | "modules/viz/test/tests_simple.cpp" | |
480 | "modules/viz/test/test_viz3d.cpp") | |
481 | (("(TEST\\(Viz, )([a-z].*\\).*)" all pre post) | |
482 | (string-append pre "DISABLED_" post))) | |
483 | ||
484 | ;; This one fails with "unknown file: Failure" | |
485 | ;; But I couldn't figure out which file was missing: | |
6c56e9c4 | 486 | (substitute* "../opencv-contrib/modules/face/test/test_face_align.cpp" |
62834314 BH |
487 | (("(TEST\\(CV_Face_FacemarkKazemi, )(can_detect_landmarks\\).*)" |
488 | all pre post) | |
489 | (string-append pre "DISABLED_" post))) | |
490 | ||
491 | ;; Failure reason: Bad accuracy | |
492 | ;; Incorrect count of accurate poses [2nd case]: 90.000000 / 94.000000 | |
6c56e9c4 | 493 | (substitute* "../opencv-contrib/modules/rgbd/test/test_odometry.cpp" |
62834314 BH |
494 | (("(TEST\\(RGBD_Odometry_Rgbd, )(algorithmic\\).*)" all pre post) |
495 | (string-append pre "DISABLED_" post))) | |
496 | #t)) | |
497 | ||
62834314 BH |
498 | (add-after 'unpack 'unpack-submodule-sources |
499 | (lambda* (#:key inputs #:allow-other-keys) | |
500 | (mkdir "../opencv-extra") | |
501 | (mkdir "../opencv-contrib") | |
6c56e9c4 EF |
502 | (copy-recursively (assoc-ref inputs "opencv-extra") |
503 | "../opencv-extra") | |
504 | (invoke "tar" "xvf" | |
505 | (assoc-ref inputs "opencv-contrib") | |
506 | "--strip-components=1" | |
507 | "-C" "../opencv-contrib"))) | |
62834314 BH |
508 | |
509 | (add-after 'set-paths 'add-ilmbase-include-path | |
510 | (lambda* (#:key inputs #:allow-other-keys) | |
511 | ;; OpenEXR propagates ilmbase, but its include files do not appear | |
512 | ;; in the CPATH, so we need to add "$ilmbase/include/OpenEXR/" to | |
513 | ;; the CPATH to satisfy the dependency on "ImathVec.h". | |
514 | (setenv "CPATH" | |
515 | (string-append (assoc-ref inputs "ilmbase") | |
516 | "/include/OpenEXR" | |
517 | ":" (or (getenv "CPATH") ""))) | |
518 | #t)) | |
519 | (add-before 'check 'start-xserver | |
520 | (lambda* (#:key inputs #:allow-other-keys) | |
521 | (let ((xorg-server (assoc-ref inputs "xorg-server")) | |
522 | (disp ":1")) | |
523 | (setenv "HOME" (getcwd)) | |
524 | (setenv "DISPLAY" disp) | |
525 | ;; There must be a running X server and make check doesn't start one. | |
526 | ;; Therefore we must do it. | |
527 | (zero? (system (format #f "~a/bin/Xvfb ~a &" xorg-server disp))))))))) | |
528 | (native-inputs | |
6c56e9c4 | 529 | `(("pkg-config" ,pkg-config) |
ff337525 | 530 | ("xorg-server" ,xorg-server-for-tests) ; For running the tests |
62834314 BH |
531 | ("opencv-extra" |
532 | ,(origin | |
6c56e9c4 EF |
533 | (method git-fetch) |
534 | (uri (git-reference | |
535 | (url "https://github.com/opencv/opencv_extra") | |
536 | (commit version))) | |
537 | (file-name (git-file-name "opencv_extra" version)) | |
62834314 | 538 | (sha256 |
6c56e9c4 | 539 | (base32 "08p5xnq8n1jw8svvz0fnirfg7q8dm3p4a5dl7527s5xj0f9qn7lp")))) |
62834314 BH |
540 | ("opencv-contrib" |
541 | ,(origin | |
6c56e9c4 EF |
542 | (method git-fetch) |
543 | (uri (git-reference | |
544 | (url "https://github.com/opencv/opencv_contrib") | |
545 | (commit version))) | |
546 | (file-name (git-file-name "opencv_contrib" version)) | |
8e21fa0b | 547 | (patches (search-patches "opencv-rgbd-aarch64-test-fix.patch")) |
62834314 | 548 | (sha256 |
6c56e9c4 | 549 | (base32 "1f334glf39nk42mpqq6j732h3ql2mpz89jd4mcl678s8n73nfjh2")))))) |
4bd428a7 | 550 | (inputs `(("libjpeg" ,libjpeg-turbo) |
62834314 BH |
551 | ("libpng" ,libpng) |
552 | ("jasper" ,jasper) | |
553 | ;; ffmpeg 4.0 causes core dumps in tests. | |
554 | ("ffmpeg" ,ffmpeg-3.4) | |
555 | ("libtiff" ,libtiff) | |
556 | ("hdf5" ,hdf5) | |
557 | ("libgphoto2" ,libgphoto2) | |
558 | ("libwebp" ,libwebp) | |
559 | ("zlib" ,zlib) | |
560 | ("gtkglext" ,gtkglext) | |
561 | ("openexr" ,openexr) | |
562 | ("ilmbase" ,ilmbase) | |
563 | ("gtk+" ,gtk+-2) | |
564 | ("python-numpy" ,python-numpy) | |
565 | ("protobuf" ,protobuf) | |
566 | ("vtk" ,vtk) | |
567 | ("python" ,python))) | |
5834e4b7 BH |
568 | ;; These three CVEs are not a problem of OpenCV, see: |
569 | ;; https://github.com/opencv/opencv/issues/10998 | |
570 | (properties '((lint-hidden-cve . ("CVE-2018-7712" | |
571 | "CVE-2018-7713" | |
572 | "CVE-2018-7714")))) | |
62834314 BH |
573 | (synopsis "Computer vision library") |
574 | (description "OpenCV is a library aimed at | |
575 | real-time computer vision, including several hundred computer | |
576 | vision algorithms. It can be used to do things like: | |
577 | ||
578 | @itemize | |
579 | @item image and video input and output | |
580 | @item image and video processing | |
581 | @item displaying | |
582 | @item feature recognition | |
583 | @item segmentation | |
584 | @item facial recognition | |
585 | @item stereo vision | |
586 | @item structure from motion | |
587 | @item augmented reality | |
588 | @item machine learning | |
589 | @end itemize\n") | |
590 | (home-page "https://opencv.org/") | |
591 | (license license:bsd-3))) | |
5bbd6931 L |
592 | |
593 | (define-public vips | |
594 | (package | |
595 | (name "vips") | |
cc33f50d | 596 | (version "8.10.6") |
7e52321f TGR |
597 | (source |
598 | (origin | |
599 | (method url-fetch) | |
600 | (uri (string-append | |
601 | "https://github.com/libvips/libvips/releases/download/v" | |
602 | version "/vips-" version ".tar.gz")) | |
603 | (sha256 | |
cc33f50d | 604 | (base32 "0vjsh3i0861f6h9as3bch956cidz824zz499pvhjs3lfjn6hhs14")))) |
5bbd6931 L |
605 | (build-system gnu-build-system) |
606 | (native-inputs | |
5d99167a EF |
607 | `(("gobject-introspection" ,gobject-introspection) |
608 | ("pkg-config" ,pkg-config))) | |
5bbd6931 | 609 | (inputs |
5d99167a EF |
610 | `(("expat" ,expat) |
611 | ("fftw" ,fftw) | |
612 | ("giflib" ,giflib) | |
613 | ("glib" ,glib) | |
614 | ("hdf5" ,hdf5) | |
615 | ("imagemagick" ,imagemagick) | |
616 | ("lcms" ,lcms) | |
617 | ("libexif" ,libexif) | |
618 | ("libgsf" ,libgsf) | |
4bd428a7 | 619 | ("libjpeg" ,libjpeg-turbo) |
5bbd6931 L |
620 | ("libpng" ,libpng) |
621 | ("librsvg" ,librsvg) | |
622 | ("libtiff" ,libtiff) | |
5d99167a | 623 | ("libxml2" ,libxml2) |
5bbd6931 | 624 | ("libwebp" ,libwebp) |
5d99167a | 625 | ("matio" ,matio) |
5bbd6931 L |
626 | ("niftilib" ,niftilib) |
627 | ("openexr" ,openexr) | |
628 | ("orc" ,orc) | |
5d99167a EF |
629 | ("pango" ,pango) |
630 | ("poppler" ,poppler))) | |
5bbd6931 | 631 | (home-page "https://libvips.github.io/libvips/") |
85e2f212 | 632 | (synopsis "Multithreaded image processing system with low memory needs") |
37c1cf89 | 633 | (description |
85e2f212 TGR |
634 | "VIPS is a demand-driven, horizontally threaded image processing library. |
635 | It's particularly good at processing large images, working with colour, | |
636 | scientific analysis, and general research & development. | |
637 | ||
638 | Compared to most image processing libraries VIPS needs little RAM and runs | |
639 | quickly, especially on machines with more than one CPU core. This is primarily | |
640 | due to its architecture which automatically parallelises the image workflows.") | |
5bbd6931 | 641 | (license license:lgpl2.1+))) |
e506b5e9 | 642 | |
657f8535 VM |
643 | (define-public gmic |
644 | (package | |
645 | (name "gmic") | |
ce9fe5f9 | 646 | (version "2.9.7") |
657f8535 VM |
647 | (source |
648 | (origin | |
649 | (method url-fetch) | |
650 | (uri (string-append "https://gmic.eu/files/source/gmic_" | |
651 | version ".tar.gz")) | |
652 | (sha256 | |
ce9fe5f9 | 653 | (base32 "05kzaplsl5qvxs7v6g73q0lq8dii8g6v77ap609188m7gr43f9cl")))) |
657f8535 VM |
654 | (build-system cmake-build-system) |
655 | (arguments | |
75862a9e VM |
656 | `(#:tests? #f ;there are no tests |
657 | #:configure-flags '("-DBUILD_LIB_STATIC=OFF" | |
658 | "-DENABLE_DYNAMIC_LINKING=ON" | |
659 | "-DENABLE_LTO=ON") | |
660 | #:phases | |
661 | (modify-phases %standard-phases | |
662 | (add-before 'configure 'set-LDFLAGS | |
663 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
664 | (setenv "LDFLAGS" | |
665 | (string-append | |
666 | "-Wl,-rpath=" | |
667 | (assoc-ref outputs "out") "/lib"))))))) | |
657f8535 VM |
668 | (native-inputs |
669 | `(("pkg-config" ,pkg-config))) | |
670 | (inputs | |
671 | `(("curl" ,curl) | |
672 | ("fftw" ,fftw) | |
673 | ("graphicsmagick" ,graphicsmagick) | |
674 | ("libjpeg-turbo" ,libjpeg-turbo) | |
675 | ("libpng" ,libpng) | |
676 | ("libtiff" ,libtiff) | |
677 | ("libx11" ,libx11) | |
678 | ;;("opencv" ,opencv) ;OpenCV is currently broken in the CI | |
679 | ("openexr" ,openexr) | |
680 | ("zlib" ,zlib))) | |
681 | (home-page "https://gmic.eu/") | |
682 | (synopsis "Full-featured framework for digital image processing") | |
683 | (description "G'MIC is a full-featured framework for digital image | |
684 | processing. It provides several user interfaces to convert / manipulate | |
685 | / filter / visualize generic image datasets, ranging from 1D scalar | |
686 | signals to 3D+t sequences of multi-spectral volumetric images, hence | |
687 | including 2D color images.") | |
688 | ;; Dual-licensed, either license applies. | |
689 | (license (list license:cecill license:cecill-c)))) | |
690 | ||
f23ba5d9 VM |
691 | (define-public gmic-qt |
692 | (package | |
693 | (inherit gmic) | |
694 | (name "gmic-qt") | |
695 | (arguments | |
696 | (substitute-keyword-arguments (package-arguments gmic) | |
697 | ((#:configure-flags _) | |
698 | `(list "-DGMIC_QT_HOST=none" "-DENABLE_DYNAMIC_LINKING=ON" | |
699 | (string-append "-DGMIC_LIB_PATH=" | |
700 | (assoc-ref %build-inputs "gmic") "/lib"))) | |
701 | ((#:phases phases) | |
702 | `(modify-phases ,phases | |
703 | (add-after 'unpack 'qt-chdir | |
704 | (lambda _ (chdir "gmic-qt") #t)))))) | |
705 | (native-inputs | |
706 | `(("pkg-config" ,pkg-config) | |
707 | ("qttools" ,qttools))) | |
708 | (inputs | |
709 | `(("gmic" ,gmic) | |
ea0a5107 | 710 | ("qtbase" ,qtbase-5) |
f23ba5d9 VM |
711 | ,@(package-inputs gmic))) |
712 | (synopsis "Qt frontend for the G'MIC image processing framework") | |
713 | (license license:gpl3+))) | |
714 | ||
78e99ae6 VM |
715 | (define-public gmic-qt-krita |
716 | (package | |
717 | (inherit gmic-qt) | |
718 | (name "gmic-qt-krita") | |
719 | (arguments | |
720 | (substitute-keyword-arguments (package-arguments gmic-qt) | |
721 | ((#:configure-flags flags) | |
722 | '(list "-DGMIC_QT_HOST=krita" "-DENABLE_DYNAMIC_LINKING=ON" | |
723 | (string-append "-DGMIC_LIB_PATH=" | |
724 | (assoc-ref %build-inputs "gmic") "/lib"))))) | |
725 | (synopsis "Krita plugin for the G'MIC image processing framework"))) | |
726 | ||
e506b5e9 L |
727 | (define-public nip2 |
728 | (package | |
729 | (name "nip2") | |
f2d3d742 | 730 | (version "8.7.1") |
e506b5e9 L |
731 | (source |
732 | (origin | |
733 | (method url-fetch) | |
734 | (uri (string-append "https://github.com/libvips/nip2/releases/download/v" | |
735 | version "/nip2-" version ".tar.gz" )) | |
736 | (sha256 | |
f2d3d742 | 737 | (base32 "0l7n427njif53npqn02gfjjly8y3khbrkzqxp10j5vp9h97psgiw")))) |
e506b5e9 L |
738 | (build-system gnu-build-system) |
739 | (arguments | |
740 | `(#:phases | |
741 | (modify-phases %standard-phases | |
f2d3d742 | 742 | ;; test_conv.ws keep failing so disabling for now. |
e506b5e9 L |
743 | (add-after 'unpack 'disable-test-conv |
744 | (lambda _ | |
745 | (delete-file "test/workspaces/test_conv.ws") | |
746 | #t)) | |
747 | (add-before 'check 'set-home | |
748 | (lambda _ | |
749 | (setenv "HOME" "/tmp") #t))))) | |
750 | (inputs | |
751 | `(("vips" ,vips) | |
752 | ("glib" ,glib) | |
753 | ("libtiff" ,libtiff) | |
754 | ("gtk+-2" ,gtk+-2) | |
755 | ("libxml2" ,libxml2) | |
756 | ("libexif" ,libexif) | |
4bd428a7 | 757 | ("libjpeg" ,libjpeg-turbo) ;required by vips.pc |
e506b5e9 L |
758 | ("librsvg" ,librsvg) |
759 | ("fftw" ,fftw) | |
760 | ("libgsf" ,libgsf) | |
761 | ("imagemagick" ,imagemagick) | |
762 | ("orc" ,orc) | |
763 | ("matio" ,matio) | |
764 | ("lcms" ,lcms) | |
765 | ("libwebp" ,libwebp) | |
766 | ("openexr" ,openexr) | |
767 | ("poppler" ,poppler) | |
768 | ("gsl" ,gsl))) | |
769 | (native-inputs | |
770 | `(("flex" ,flex) | |
771 | ("bison" ,bison) | |
772 | ("pkg-config" ,pkg-config))) | |
773 | (home-page "https://github.com/libvips/nip2") | |
774 | (synopsis "Spreadsheet-like GUI for libvips") | |
775 | (description "This package provide a graphical user interface (GUI) for | |
776 | the VIPS image processing library. It's a little like a spreadsheet: you | |
777 | create a set of formula connecting your objects together, and on a change nip2 | |
778 | recalculates.") | |
779 | (license license:gpl2+))) | |
02e1acfb RW |
780 | |
781 | (define-public vxl | |
782 | (package | |
783 | (name "vxl") | |
784 | (version "2.0.2") | |
785 | (source | |
786 | (origin | |
787 | (method git-fetch) | |
788 | (uri (git-reference | |
b0e7b699 | 789 | (url "https://github.com/vxl/vxl") |
02e1acfb RW |
790 | (commit (string-append "v" version)))) |
791 | (file-name (git-file-name name version)) | |
792 | (sha256 | |
793 | (base32 "0949hw57szq8943f1whwqaz591xjmb19kj803hcv74hdai2b0ycg")) | |
794 | (modules '((guix build utils))) | |
795 | ;; TODO: vxl includes an old version of dcmtk. It won't build with | |
796 | ;; version 3.6.x. | |
797 | (snippet | |
798 | '(begin | |
799 | (for-each delete-file-recursively | |
800 | '("v3p/bzlib/" | |
801 | "v3p/geotiff/" | |
802 | "v3p/jpeg/" | |
803 | "v3p/png/" | |
804 | "v3p/tiff/" | |
805 | "v3p/zlib/")) | |
806 | (substitute* "v3p/CMakeLists.txt" | |
807 | (("add_subdirectory\\((tiff|png|jpeg|zlib|bzlib|geotiff)\\)") | |
808 | "")) | |
809 | #t)))) | |
810 | (build-system cmake-build-system) | |
811 | (inputs | |
812 | `(("libgeotiff" ,libgeotiff) | |
813 | ("libtiff" ,libtiff) | |
4bd428a7 | 814 | ("libjpeg" ,libjpeg-turbo) |
02e1acfb RW |
815 | ("libpng" ,libpng) |
816 | ("zlib" ,zlib))) | |
817 | (home-page "https://github.com/vxl/vxl/") | |
818 | (synopsis "Collection of C++ libraries for computer vision") | |
819 | (description "VXL (the Vision-something-Libraries) is a collection of C++ | |
820 | libraries designed for computer vision research and implementation.") | |
821 | (license license:bsd-3))) | |
4243af4e RW |
822 | |
823 | (define-public vxl-1 | |
824 | (package (inherit vxl) | |
825 | (name "vxl") | |
826 | (version "1.18.0") | |
827 | (source | |
828 | (origin | |
829 | (method git-fetch) | |
830 | (uri (git-reference | |
b0e7b699 | 831 | (url "https://github.com/vxl/vxl") |
4243af4e RW |
832 | (commit (string-append "v" version)))) |
833 | (file-name (git-file-name name version)) | |
834 | (sha256 | |
835 | (base32 "1g4mr2cc58jwm0vasscbd4y5380wj3ahkvq121z4gs83fhavvxgz")) | |
836 | (modules '((guix build utils))) | |
837 | (snippet | |
838 | '(begin | |
839 | (for-each delete-file-recursively | |
840 | '("v3p/bzlib/" | |
841 | "v3p/geotiff/" | |
842 | "v3p/png/" | |
843 | "v3p/tiff/" | |
844 | "v3p/zlib/")) | |
845 | (substitute* "v3p/CMakeLists.txt" | |
846 | (("add_subdirectory\\((tiff|png|jpeg|zlib|bzlib|geotiff)\\)") | |
847 | "")) | |
848 | #t)))) | |
849 | (arguments | |
850 | `(#:configure-flags | |
851 | ;; Needed for itk-snap | |
852 | (list "-DVNL_CONFIG_LEGACY_METHODS=ON"))))) | |
d7701e1b RW |
853 | |
854 | (define-public insight-toolkit | |
855 | (package | |
856 | (name "insight-toolkit") | |
857 | (version "5.0.0") | |
858 | (source | |
859 | (origin | |
860 | (method url-fetch) | |
861 | (uri (string-append "https://github.com/InsightSoftwareConsortium/ITK/" | |
862 | "releases/download/v" version "/InsightToolkit-" | |
863 | version ".tar.xz")) | |
864 | (sha256 | |
865 | (base32 "0bs63mk4q8jmx38f031jy5w5n9yy5ng9x8ijwinvjyvas8cichqi")))) | |
866 | (build-system cmake-build-system) | |
867 | (arguments | |
868 | `(#:tests? #f ; tests require network access and external data | |
869 | #:configure-flags | |
870 | '("-DITK_USE_GPU=ON" | |
871 | "-DITK_USE_SYSTEM_LIBRARIES=ON" | |
872 | "-DITK_USE_SYSTEM_GOOGLETEST=ON" | |
873 | "-DITK_BUILD_SHARED=ON" | |
874 | ;; This prevents "GTest::GTest" from being added to the ITK_LIBRARIES | |
875 | ;; variable in the installed CMake files. This is necessary as other | |
876 | ;; packages using insight-toolkit could not be configured otherwise. | |
877 | "-DGTEST_ROOT=gtest") | |
d769fcd6 | 878 | |
d7701e1b RW |
879 | #:phases |
880 | (modify-phases %standard-phases | |
881 | (add-after 'unpack 'do-not-tune | |
882 | (lambda _ | |
883 | (substitute* "CMake/ITKSetStandardCompilerFlags.cmake" | |
884 | (("-mute=native") "")) | |
885 | #t))))) | |
886 | (inputs | |
887 | `(("eigen" ,eigen) | |
888 | ("expat" ,expat) | |
889 | ("fftw" ,fftw) | |
890 | ("fftwf" ,fftwf) | |
891 | ("hdf5" ,hdf5) | |
4bd428a7 | 892 | ("libjpeg" ,libjpeg-turbo) |
d7701e1b RW |
893 | ("libpng" ,libpng) |
894 | ("libtiff" ,libtiff) | |
895 | ("mesa" ,mesa-opencl) | |
896 | ("perl" ,perl) | |
897 | ("python" ,python) | |
898 | ("tbb" ,tbb) | |
899 | ("vxl" ,vxl-1) | |
900 | ("zlib" ,zlib))) | |
901 | (native-inputs | |
902 | `(("googletest" ,googletest) | |
903 | ("pkg-config" ,pkg-config))) | |
904 | (home-page "https://github.com/InsightSoftwareConsortium/ITK/") | |
905 | (synopsis "Scientific image processing, segmentation and registration") | |
906 | (description "The Insight Toolkit (ITK) is a toolkit for N-dimensional | |
907 | scientific image processing, segmentation, and registration. Segmentation is | |
908 | the process of identifying and classifying data found in a digitally sampled | |
909 | representation. Typically the sampled representation is an image acquired | |
910 | from such medical instrumentation as CT or MRI scanners. Registration is the | |
911 | task of aligning or developing correspondences between data. For example, in | |
912 | the medical environment, a CT scan may be aligned with a MRI scan in order to | |
913 | combine the information contained in both.") | |
914 | (license license:asl2.0))) | |
8f4d457d RW |
915 | |
916 | (define-public insight-toolkit-4 | |
917 | (package (inherit insight-toolkit) | |
918 | (version "4.13.2") | |
919 | (source | |
920 | (origin | |
921 | (method url-fetch) | |
922 | (uri (string-append "https://github.com/InsightSoftwareConsortium/ITK/" | |
923 | "releases/download/v" version "/InsightToolkit-" | |
924 | version ".tar.xz")) | |
925 | (sha256 | |
926 | (base32 "19cgfpd63gqrvc3m27m394gy2d7w79g5y6lvznb5qqr49lihbgns")))) | |
927 | (arguments | |
928 | `(#:tests? #f ; tests require network access and external data | |
929 | #:configure-flags | |
930 | '("-DITKV3_COMPATIBILITY=ON" ; needed for itk-snap | |
931 | "-DITK_USE_GPU=ON" | |
932 | "-DITK_USE_SYSTEM_LIBRARIES=ON" | |
933 | "-DITK_USE_SYSTEM_GOOGLETEST=ON" | |
934 | "-DITK_USE_SYSTEM_VXL=ON"))))) | |
07f36b0c RW |
935 | |
936 | (define-public insight-toolkit-4.12 | |
937 | (package (inherit insight-toolkit-4) | |
938 | (version "4.12.2") | |
939 | (source | |
940 | (origin | |
941 | (method url-fetch) | |
942 | (uri (string-append "mirror://sourceforge/itk/itk/4.12/" | |
943 | "InsightToolkit-" version ".tar.xz")) | |
944 | (sha256 | |
945 | (base32 "1qw9mxbh083siljygahl4gdfv91xvfd8hfl7ghwii19f60xrvn2w")))))) | |
1c4e6aa9 RW |
946 | |
947 | (define-public itk-snap | |
948 | (package | |
949 | (name "itk-snap") | |
950 | (version "3.8.0") | |
951 | (source | |
952 | (origin | |
953 | (method git-fetch) | |
954 | (uri (git-reference | |
955 | (url "https://git.code.sf.net/p/itk-snap/src") | |
956 | (commit (string-append "v" version)))) | |
957 | (file-name (git-file-name name version)) | |
958 | (sha256 | |
959 | (base32 "15i5ixpryfrbf3vrrb5rici8fb585f25k0v1ljds16bp1f1msr4q")))) | |
960 | (build-system cmake-build-system) | |
961 | (arguments | |
962 | `(#:configure-flags | |
963 | (list "-DSNAP_VERSION_GIT_SHA1=release" | |
964 | "-DSNAP_VERSION_GIT_BRANCH=release" | |
965 | "-DSNAP_VERSION_GIT_TIMESTAMP=0" | |
966 | "-DSNAP_PACKAGE_QT_PLUGINS=OFF" | |
0fe041bd | 967 | "-DCMAKE_POSITION_INDEPENDENT_CODE=ON") |
1c4e6aa9 RW |
968 | #:phases |
969 | (modify-phases %standard-phases | |
970 | ;; During the installation phase all libraries provided by all | |
971 | ;; dependencies will be copied to the lib directory. That's insane, | |
972 | ;; so we disable this. | |
973 | (add-after 'unpack 'do-not-copy-dependencies | |
974 | (lambda _ | |
975 | (substitute* "CMakeLists.txt" | |
976 | (("install_qt5_executable\ | |
977 | \\(\\$\\{SNAP_MAIN_INSTALL_DIR\\}/\\$\\{SNAP_EXE\\}\\)") | |
978 | "")) | |
979 | #t)) | |
980 | (add-after 'unpack 'disable-gui-tests | |
981 | (lambda _ | |
982 | ;; The GUI tests just time out. | |
983 | (substitute* "CMakeLists.txt" | |
984 | ((" (Workspace|DiffSpace|ProbeIntensity|RegionCompetition\ | |
985 | |RandomForest|RandomForestBailOut)") | |
986 | "")) | |
987 | #t)) | |
988 | (add-after 'unpack 'make-reproducible | |
989 | (lambda _ | |
990 | (substitute* "CMakeLists.txt" | |
991 | (("TODAY\\(SNAP_VERSION_COMPILE_DATE\\)") | |
992 | "SET(SNAP_VERSION_COMPILE_DATE \"(removed for reproducibility)\")")) | |
993 | #t)) | |
994 | (add-after 'unpack 'prepare-submodules | |
995 | (lambda* (#:key inputs #:allow-other-keys) | |
996 | (rmdir "Submodules/c3d") | |
997 | (copy-recursively (assoc-ref inputs "c3d-src") | |
998 | "Submodules/c3d") | |
999 | (substitute* '("Submodules/c3d/adapters/BiasFieldCorrectionN4.cxx" | |
1000 | "Submodules/c3d/adapters/ApplyMetric.cxx") | |
1001 | (("vcl_") "std::")) | |
1002 | (rmdir "Submodules/greedy") | |
1003 | (symlink (assoc-ref inputs "greedy-src") | |
1004 | "Submodules/greedy") | |
1005 | #t)) | |
1006 | (add-after 'unpack 'fix-includes | |
1007 | (lambda _ | |
1008 | (substitute* "GUI/Model/RegistrationModel.cxx" | |
1009 | (("<vnl_symmetric_eigensystem.h>") | |
1010 | "<vnl/algo/vnl_symmetric_eigensystem.h>")) | |
1011 | #t)) | |
1012 | (add-before 'check 'prepare-tests | |
1013 | (lambda _ | |
1014 | ;; Needed by at least one test. | |
1015 | (setenv "HOME" "/tmp") | |
1016 | #t)) | |
1017 | (add-after 'install 'wrap-executable | |
1018 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
1019 | (let ((out (assoc-ref outputs "out"))) | |
1020 | (wrap-program (string-append out "/bin/itksnap") | |
1021 | `("QT_PLUGIN_PATH" ":" prefix | |
1022 | ,(map (lambda (label) | |
1023 | (string-append (assoc-ref inputs label) | |
1024 | "/lib/qt5/plugins")) | |
1025 | '("qtbase" "qtdeclarative")))) | |
1026 | #t)))))) | |
1027 | (inputs | |
1028 | `(("curl" ,curl) | |
1029 | ("fftw" ,fftw) | |
1030 | ("fftwf" ,fftwf) | |
1031 | ("glu" ,glu) | |
1032 | ("hdf5" ,hdf5) | |
1033 | ("mesa" ,mesa-opencl) | |
1034 | ;; This package does not build with either insight-toolkit 5.0.0 and | |
1035 | ;; not with 4.13. It really needs to be 4.12. | |
1036 | ("itk" ,insight-toolkit-4.12) | |
1037 | ("vtk" ,vtk-6) | |
ea0a5107 | 1038 | ("qtbase" ,qtbase-5) |
1c4e6aa9 | 1039 | ("qtdeclarative" ,qtdeclarative) |
1c4e6aa9 RW |
1040 | ("vxl" ,vxl-1) |
1041 | ("zlib" ,zlib))) | |
1042 | (native-inputs | |
1043 | `(("googletest" ,googletest) | |
957e0be3 | 1044 | ("qttools" ,qttools) |
1c4e6aa9 RW |
1045 | ("pkg-config" ,pkg-config) |
1046 | ("c3d-src" | |
1047 | ,(let* ((commit "f521358db26e00002c911cc47bf463b043942ad3") | |
1048 | (revision "1") | |
1049 | (version (git-version "0" revision commit))) | |
1050 | (origin | |
1051 | (method git-fetch) | |
1052 | (uri (git-reference | |
b0e7b699 | 1053 | (url "https://github.com/pyushkevich/c3d") |
1c4e6aa9 RW |
1054 | (commit commit))) |
1055 | (file-name (git-file-name "c3d" version)) | |
1056 | (sha256 | |
1057 | (base32 | |
1058 | "0kyv3rxrxwr8c3sa9zv01lsnhk95b27gx1s870k3yi8qp52h7bx3"))))) | |
1059 | ;; We are using an arbitrary commit from 2017 because the latest | |
1060 | ;; version breaks the build... | |
1061 | ("greedy-src" | |
1062 | ,(let* ((commit "97e340f7e8e66597599144947775e6039e79a0d3") | |
1063 | (revision "1") | |
1064 | (version (git-version "0" revision commit))) | |
1065 | (origin | |
1066 | (method git-fetch) | |
1067 | (uri (git-reference | |
b0e7b699 | 1068 | (url "https://github.com/pyushkevich/greedy") |
1c4e6aa9 RW |
1069 | (commit commit))) |
1070 | (file-name (git-file-name "greedy" version)) | |
1071 | (sha256 | |
1072 | (base32 | |
1073 | "0k5bc9za4jrc8z9dj08z1rkcp5xf0gnd1d2jmi1w9ny4vxh2q2ab"))))))) | |
1074 | (home-page "https://sourceforge.net/p/itk-snap/") | |
1075 | (synopsis "Medical image segmentation") | |
1076 | (description "ITK-SNAP is a tool for segmenting anatomical structures in | |
1077 | medical images. It provides an automatic active contour segmentation | |
1078 | pipeline, along with supporting a manual segmentation toolbox. ITK-SNAP has a | |
1079 | full-featured UI aimed at clinical researchers.") | |
1080 | ;; This includes the submodules greedy and c3d. | |
1081 | (license license:gpl3+))) | |
85c4f486 PN |
1082 | |
1083 | (define-public metapixel | |
1084 | ;; Follow stable branch. | |
1085 | (let ((commit "98ee9daa093b6c334941242e63f90b1c2876eb4f")) | |
1086 | (package | |
1087 | (name "metapixel") | |
1088 | (version (git-version "1.0.2" "1" commit)) | |
1089 | (source | |
1090 | (origin | |
1091 | (method git-fetch) | |
1092 | (uri (git-reference | |
1093 | (url "https://github.com/schani/metapixel") | |
1094 | (commit commit) | |
1095 | ;; TODO: Package rwimg and lispreader? | |
1096 | (recursive? #t))) | |
1097 | (file-name (git-file-name name version)) | |
1098 | (sha256 | |
1099 | (base32 "0r7n3a6bvcxkbpda4mwmrpicii09iql5z69nkjqygkwxw7ny3309")))) | |
1100 | (build-system gnu-build-system) | |
1101 | (inputs | |
1102 | `(("giflib" ,giflib) | |
1103 | ("libjpeg" ,libjpeg-turbo) | |
1104 | ("libpng" ,libpng) | |
1105 | ("perl" ,perl))) | |
1106 | (native-inputs | |
1107 | `(("pkg-config" ,pkg-config) | |
1108 | ("docbook-xml" ,docbook-xml) | |
1109 | ("docbook-xsl" ,docbook-xsl) | |
1110 | ("xsltproc" ,libxslt))) | |
1111 | (arguments | |
1112 | `(#:tests? #f ; No tests. | |
1113 | #:make-flags (list | |
1114 | (string-append "PREFIX=" (assoc-ref %outputs "out")) | |
1115 | (string-append "MANPAGE_XSL=" | |
1116 | (assoc-ref %build-inputs "docbook-xsl") | |
1117 | "/xml/xsl/docbook-xsl-*/manpages/docbook.xsl")) | |
1118 | #:phases | |
1119 | (modify-phases %standard-phases | |
1120 | (delete 'configure) | |
1121 | (add-before 'install 'make-local-docbook-xml | |
1122 | (lambda* (#:key inputs #:allow-other-keys) | |
1123 | (substitute* "metapixel.xml" | |
1124 | (("http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd") | |
1125 | (string-append (assoc-ref inputs "docbook-xml") | |
1126 | "/xml/dtd/docbook/docbookx.dtd"))) | |
1127 | #t)) | |
1128 | (add-before 'install 'fix-directory-creation | |
1129 | (lambda* (#:key outputs #:allow-other-keys) | |
1130 | (mkdir-p (string-append (assoc-ref outputs "out") "/share/man/man1")) | |
1131 | #t))))) | |
1132 | (home-page "https://www.complang.tuwien.ac.at/schani/metapixel/") | |
1133 | (synopsis "Photomosaics generator") | |
1134 | (description "Metapixel is a program for generating photomosaics. It can | |
1135 | generate classical photomosaics, in which the source image is viewed as a | |
1136 | matrix of equally sized rectangles for each of which a matching image is | |
1b8be80e | 1137 | substituted, as well as collage-style photomosaics, in which rectangular parts |
85c4f486 PN |
1138 | of the source image at arbitrary positions (i.e. not aligned to a matrix) are |
1139 | substituted by matching images.") | |
1140 | (license license:gpl2)))) | |
a76e9d13 BT |
1141 | |
1142 | (define-public scantailor-advanced | |
1143 | (let ((commit "3d1e74e6ace413733511086934a66f4e3f7a6027")) | |
1144 | (package | |
1145 | (name "scantailor-advanced") | |
1146 | (version (string-append "1.0.16-" (string-take commit 7))) | |
1147 | (source | |
1148 | (origin | |
1149 | (method git-fetch) | |
1150 | (uri (git-reference | |
1151 | (url "https://github.com/4lex4/scantailor-advanced") | |
1152 | (commit commit))) | |
1153 | (file-name (git-file-name name version)) | |
1154 | (sha256 | |
1155 | (base32 | |
1156 | "0kixwjb2x457dq7927hkh34c803p7yh1pmn6n61rk9shqrcg492h")))) | |
1157 | (build-system qt-build-system) | |
1158 | (native-inputs | |
1159 | `(("qttools" ,qttools))) | |
1160 | (inputs | |
1161 | `(("boost" ,boost) | |
1162 | ("libjpeg" ,libjpeg-turbo) | |
1163 | ("libpng" ,libpng) | |
1164 | ("libtiff" ,libtiff) | |
ea0a5107 | 1165 | ("qtbase" ,qtbase-5) |
a76e9d13 BT |
1166 | ("qtsvg" ,qtsvg) |
1167 | ("zlib" ,zlib))) | |
1168 | (arguments | |
1169 | `(#:phases | |
1170 | (modify-phases %standard-phases | |
1171 | ;; Some tests require a display and fail with offscreen mode. | |
1172 | (add-after 'unpack 'disable-failing-tests | |
1173 | (lambda _ | |
1174 | (setenv "ARGS" "--exclude-regex \"imageproc_.*\"") | |
1175 | #t))))) | |
1176 | (home-page "https://github.com/4lex4/scantailor-advanced") | |
1177 | (synopsis "Clean up scanned pages") | |
1178 | (description "Scan Tailor is an interactive post-processing tool for | |
1179 | scanned pages. It performs operations such as page splitting, deskewing, | |
1180 | adding/removing borders, and others. You give it raw scans, and you get pages | |
1181 | ready to be printed or assembled into a PDF or DJVU file. Scanning, optical | |
1182 | character recognition, and assembling multi-page documents are out of scope of | |
1183 | this project. | |
1184 | ||
1185 | Scan Tailer Advanced is a fork of Scan Tailer that merges Scan Tailor Featured | |
1186 | and Scan Tailor Enhanced versions as well as including many more bug fixes.") | |
1187 | (license license:gpl3+)))) | |
58a5746e OM |
1188 | |
1189 | (define-public stiff | |
1190 | (package | |
1191 | (name "stiff") | |
1192 | (version "2.4.0") | |
1193 | (source | |
1194 | (origin | |
1195 | (method url-fetch) | |
1196 | (uri (string-append "https://www.astromatic.net/download/stiff/stiff-" | |
1197 | version ".tar.gz")) | |
1198 | (sha256 | |
1199 | (base32 "14m92dskzw7bwsr64ha4p0mj3ndv13gwcbfic3qxrs3zq5353s7l")))) | |
1200 | (build-system gnu-build-system) | |
1201 | (inputs | |
1202 | `(("libtiff" ,libtiff) | |
1203 | ("zlib" ,zlib) | |
1204 | ("libjpeg-turbo" ,libjpeg-turbo))) | |
1205 | (home-page "https://www.astromatic.net/software/stiff") | |
1206 | (synopsis "Convert scientific FITS images to TIFF format") | |
1207 | (description | |
1208 | "STIFF is a program that converts scientific @acronym{FITS, Flexible Image | |
1209 | Transport System} images to the more popular TIFF format for illustration | |
1210 | purposes.") | |
1211 | (license license:gpl3+))) |