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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> |
fb226b43 JD |
4 | ;;; Copyright © 2014 Ludovic Courtès <ludo@gnu.org> |
5 | ;;; Copyright © 2014 Mark H Weaver <mhw@netris.org> | |
6 | ;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.org> | |
8bf70426 | 7 | ;;; Copyright © 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr> |
62834314 | 8 | ;;; Copyright © 2018 Björn Höfling <bjoern.hoefling@bjoernhoefling.de> |
e506b5e9 | 9 | ;;; Copyright © 2018 Lprndn <guix@lprndn.info> |
6949f45c | 10 | ;;; Copyright © 2019 Efraim Flashner <efraim@flashner.co.il> |
957e0be3 | 11 | ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com> |
657f8535 | 12 | ;;; Copyright © 2020 Vinicius Monego <monego@posteo.net> |
85c4f486 | 13 | ;;; Copyright © 2020 Pierre Neidhardt <mail@ambrevar.xyz> |
504c285d JD |
14 | ;;; |
15 | ;;; This file is part of GNU Guix. | |
16 | ;;; | |
17 | ;;; GNU Guix is free software; you can redistribute it and/or modify it | |
18 | ;;; under the terms of the GNU General Public License as published by | |
19 | ;;; the Free Software Foundation; either version 3 of the License, or (at | |
20 | ;;; your option) any later version. | |
21 | ;;; | |
22 | ;;; GNU Guix is distributed in the hope that it will be useful, but | |
23 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of | |
24 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
25 | ;;; GNU General Public License for more details. | |
26 | ;;; | |
27 | ;;; You should have received a copy of the GNU General Public License | |
28 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. | |
29 | ||
30 | (define-module (gnu packages image-processing) | |
31 | #:use-module ((guix licenses) #:prefix license:) | |
32 | #:use-module (guix packages) | |
33 | #:use-module (guix utils) | |
34 | #:use-module (guix download) | |
6c56e9c4 | 35 | #:use-module (guix git-download) |
cdb2a211 | 36 | #:use-module (guix build-system cmake) |
504c285d JD |
37 | #:use-module (guix build-system gnu) |
38 | #:use-module (gnu packages) | |
cdb2a211 | 39 | #:use-module (gnu packages algebra) |
e506b5e9 | 40 | #:use-module (gnu packages bison) |
cdb2a211 | 41 | #:use-module (gnu packages boost) |
d7701e1b | 42 | #:use-module (gnu packages check) |
504c285d | 43 | #:use-module (gnu packages compression) |
1c4e6aa9 | 44 | #:use-module (gnu packages curl) |
85c4f486 | 45 | #:use-module (gnu packages docbook) |
504c285d | 46 | #:use-module (gnu packages documentation) |
e506b5e9 | 47 | #:use-module (gnu packages flex) |
fb226b43 | 48 | #:use-module (gnu packages fontutils) |
02e1acfb | 49 | #:use-module (gnu packages geo) |
5bbd6931 | 50 | #:use-module (gnu packages ghostscript) |
fb226b43 | 51 | #:use-module (gnu packages gl) |
5bbd6931 | 52 | #:use-module (gnu packages glib) |
cdb2a211 JD |
53 | #:use-module (gnu packages gnome) |
54 | #:use-module (gnu packages graphics) | |
55 | #:use-module (gnu packages graphviz) | |
5bbd6931 | 56 | #:use-module (gnu packages gstreamer) |
62834314 | 57 | #:use-module (gnu packages gtk) |
504c285d | 58 | #:use-module (gnu packages image) |
5bbd6931 | 59 | #:use-module (gnu packages imagemagick) |
cdb2a211 | 60 | #:use-module (gnu packages maths) |
5bbd6931 | 61 | #:use-module (gnu packages pdf) |
cdb2a211 | 62 | #:use-module (gnu packages perl) |
62834314 | 63 | #:use-module (gnu packages photo) |
cdb2a211 | 64 | #:use-module (gnu packages pkg-config) |
62834314 | 65 | #:use-module (gnu packages protobuf) |
cdb2a211 | 66 | #:use-module (gnu packages python) |
44d10b1f | 67 | #:use-module (gnu packages python-xyz) |
1c4e6aa9 | 68 | #:use-module (gnu packages qt) |
fb226b43 | 69 | #:use-module (gnu packages serialization) |
d7701e1b | 70 | #:use-module (gnu packages tbb) |
8486a80d | 71 | #:use-module (gnu packages tls) |
2283cf4c | 72 | #:use-module (gnu packages version-control) |
62834314 | 73 | #:use-module (gnu packages video) |
fb226b43 | 74 | #:use-module (gnu packages xiph) |
cdb2a211 | 75 | #:use-module (gnu packages xml) |
ebe0271a | 76 | #:use-module (gnu packages xorg) |
18696f7a RW |
77 | #:use-module (ice-9 match) |
78 | #:use-module (srfi srfi-1)) | |
504c285d | 79 | |
504c285d JD |
80 | (define-public dcmtk |
81 | (package | |
82 | (name "dcmtk") | |
6a04c8ff | 83 | (version "3.6.5") |
882d579d TGR |
84 | (source |
85 | (origin | |
86 | (method url-fetch) | |
87 | (uri | |
88 | (string-append "ftp://dicom.offis.de/pub/dicom/offis/software/dcmtk/" | |
89 | "dcmtk" (string-join (string-split version #\.) "") | |
90 | "/dcmtk-" version ".tar.gz")) | |
91 | (sha256 | |
6a04c8ff | 92 | (base32 "1fdyz5wwjp4grys61mxb2ia9fi6i3ax6s43l16xnv291bxk7hld0")))) |
882d579d | 93 | (build-system cmake-build-system) |
504c285d | 94 | (inputs |
8486a80d TGR |
95 | `(;; Our ICU is too recent: “error: ‘UChar’ does not name a type“. |
96 | ;; ("icu4c" ,icu4c) | |
4bd428a7 | 97 | ("libjpeg" ,libjpeg-turbo) |
504c285d | 98 | ("libpng" ,libpng) |
882d579d | 99 | ("libtiff" ,libtiff) |
8486a80d TGR |
100 | ("libxml2" ,libxml2) |
101 | ("openssl" ,openssl) | |
504c285d JD |
102 | ("zlib" ,zlib))) |
103 | (native-inputs | |
882d579d | 104 | `(("doxygen" ,doxygen))) ; for HTML documentation |
d2ad4f2e | 105 | (home-page "https://dcmtk.org") |
504c285d JD |
106 | (synopsis "Libraries and programs implementing parts of the DICOM standard") |
107 | (description "DCMTK is a collection of libraries and applications | |
108 | implementing large parts the DICOM standard. It includes software for | |
109 | examining, constructing and converting DICOM image files, handling offline | |
110 | media, sending and receiving images over a network connection, as well as | |
111 | demonstrative image storage and worklist servers.") | |
112 | (license (license:fsf-free | |
113 | "file://COPYRIGHT" | |
114 | "A union of the Apache 2.0 licence and various non-copyleft | |
115 | licences similar to the Modified BSD licence.")))) | |
cdb2a211 JD |
116 | |
117 | (define-public mia | |
118 | (package | |
119 | (name "mia") | |
11861d2b | 120 | (version "2.4.6") |
cdb2a211 JD |
121 | (source (origin |
122 | (method url-fetch) | |
123 | (uri (string-append "mirror://sourceforge/mia/mia/" | |
124 | (version-major+minor version) | |
125 | "/mia-" version ".tar.xz")) | |
126 | (sha256 | |
127 | (base32 | |
11861d2b | 128 | "0j4nd5z7i3v199jh7hqqhwd4g7snchizkc7rhzanpvngqg91m1pb")))) |
cdb2a211 JD |
129 | (build-system cmake-build-system) |
130 | (arguments | |
131 | `(#:configure-flags | |
132 | (list "-DMIA_CREATE_NIPYPE_INTERFACES=0" | |
cdb2a211 JD |
133 | "-DCMAKE_CXX_FLAGS=-fpermissive"))) |
134 | (inputs | |
135 | `(("boost" ,boost) | |
136 | ("dcmtk" ,dcmtk) | |
137 | ("doxygen" ,doxygen) | |
138 | ("eigen" ,eigen) | |
139 | ("fftw" ,fftw) | |
140 | ("fftwf" ,fftwf) | |
141 | ("gsl" ,gsl) | |
142 | ("gts" ,gts) | |
143 | ("hdf5" ,hdf5) | |
144 | ("itpp" ,itpp) | |
4bd428a7 | 145 | ("libjpeg" ,libjpeg-turbo) |
cdb2a211 JD |
146 | ("libpng" ,libpng) |
147 | ("libtiff" ,libtiff) | |
148 | ("libxml" ,libxml2) | |
149 | ("libxml++" ,libxml++) | |
150 | ("maxflow" ,maxflow) | |
151 | ("niftilib" ,niftilib) | |
152 | ("nlopt" ,nlopt) | |
153 | ("openexr" ,openexr) | |
154 | ("python-lxml" ,python2-lxml) | |
155 | ("vtk" ,vtk))) | |
156 | (native-inputs | |
157 | `(("pkg-config" ,pkg-config) | |
158 | ("python" ,python-2))) | |
159 | (home-page "http://mia.sourceforge.net") | |
160 | (synopsis "Toolkit for gray scale medical image analysis") | |
161 | (description "MIA provides a combination of command line tools, plug-ins, | |
162 | and libraries that make it possible run image processing tasks interactively | |
163 | in a command shell and to prototype using the shell's scripting language. It | |
164 | is built around a plug-in structure that makes it easy to add functionality | |
165 | without compromising the original code base and it makes use of a wide variety | |
166 | of external libraries that provide additional functionality.") | |
167 | (license license:gpl3+))) | |
fb226b43 | 168 | |
2283cf4c TGR |
169 | (define-public opencolorio |
170 | (package | |
171 | (name "opencolorio") | |
172 | (version "1.1.1") | |
173 | (source | |
174 | (origin | |
175 | (method git-fetch) | |
176 | (uri (git-reference | |
177 | (url "https://github.com/AcademySoftwareFoundation/OpenColorIO") | |
178 | (commit (string-append "v" version)))) | |
179 | (sha256 | |
180 | (base32 "12srvxca51czpfjl0gabpidj9n84mw78ivxy5w75qhq2mmc798sb")) | |
181 | (file-name (git-file-name name version)) | |
182 | (modules '((guix build utils))) | |
183 | (snippet | |
184 | `(begin | |
185 | ;; Remove bundled tarballs, patches, and .jars(!). XXX: Upstream | |
186 | ;; claims to have fixed USE_EXTERNAL_YAML, but it still fails with: | |
187 | ;; https://github.com/AcademySoftwareFoundation/OpenColorIO/issues/517 | |
188 | ;; When removing it, also remove it from the licence field comment. | |
189 | (for-each delete-file-recursively | |
190 | (filter | |
191 | (lambda (full-name) | |
192 | (let ((file (basename full-name))) | |
193 | (not (or (string-prefix? "yaml-cpp-0.3" file) | |
194 | (string=? "unittest.h" file))))) | |
195 | (find-files "ext" ".*"))) | |
196 | ||
197 | #t)))) | |
198 | (build-system cmake-build-system) | |
199 | (arguments | |
200 | `(#:configure-flags | |
201 | (list (string-append "-DCMAKE_CXX_FLAGS=" | |
202 | "-Wno-error=deprecated-declarations " | |
203 | "-Wno-error=unused-function") | |
204 | "-DOCIO_BUILD_STATIC=OFF" | |
205 | ;; "-DUSE_EXTERNAL_YAML=ON" | |
206 | "-DUSE_EXTERNAL_TINYXML=ON" | |
207 | "-DUSE_EXTERNAL_LCMS=ON") | |
208 | #:phases | |
209 | (modify-phases %standard-phases | |
210 | (add-after 'unpack 'patch-test-suite | |
211 | (lambda _ | |
212 | (substitute* "src/core_tests/CMakeLists.txt" | |
213 | (("/bin/sh") (which "bash"))) | |
214 | #t))))) | |
215 | (native-inputs | |
216 | `(("git" ,git) | |
217 | ("pkg-config" ,pkg-config))) | |
218 | (inputs | |
219 | ;; XXX Adding freeglut, glew, ilmbase, mesa, and openimageio for | |
220 | ;; ocioconvert fails: error: conflicting declaration ?typedef void | |
221 | ;; (* PFNGLGETFRAGMENTMATERIALFVSGIXPROC)(GLenum, GLenum, GLfloat*) | |
222 | `(("lcms" ,lcms) | |
223 | ("openexr" ,openexr) | |
224 | ("tinyxml" ,tinyxml))) | |
225 | (home-page "https://opencolorio.org") | |
226 | (synopsis "Color management for visual effects and animation") | |
227 | (description | |
228 | "OpenColorIO, or OCIO, is a complete color management solution geared | |
229 | towards motion picture production, with an emphasis on visual effects and | |
230 | computer animation. It provides a straightforward and consistent user | |
231 | experience across all supporting applications while allowing for sophisticated | |
232 | back-end configuration options suitable for high-end production usage. | |
233 | ||
234 | OCIO is compatible with the @acronym{ACES, Academy Color Encoding | |
235 | Specification} and is @acronym{LUT, look-up table}-format agnostic, supporting | |
236 | many popular formats.") | |
237 | (license (list license:expat ; docs/ociotheme/static, ext/yaml-cpp-* | |
238 | license:zlib ; src/core/md5 | |
239 | license:bsd-3)))) ; the rest | |
240 | ||
fb226b43 JD |
241 | (define-public vtk |
242 | (package | |
243 | (name "vtk") | |
8f8bc406 | 244 | (version "8.2.0") |
fb226b43 JD |
245 | (source (origin |
246 | (method url-fetch) | |
f1d4f264 | 247 | (uri (string-append "https://vtk.org/files/release/" |
fb226b43 JD |
248 | (version-major+minor version) |
249 | "/VTK-" version ".tar.gz")) | |
250 | (sha256 | |
251 | (base32 | |
8f8bc406 | 252 | "1fspgp8k0myr6p2a6wkc21ldcswb4bvmb484m12mxgk1a9vxrhrl")))) |
fb226b43 JD |
253 | (build-system cmake-build-system) |
254 | (arguments | |
255 | '(#:build-type "Release" ;Build without '-g' to save space. | |
256 | ;; -DVTK_USE_SYSTEM_NETCDF:BOOL=TRUE requires netcdf_cxx | |
257 | #:configure-flags '("-DVTK_USE_SYSTEM_EXPAT:BOOL=TRUE" | |
258 | "-DVTK_USE_SYSTEM_FREETYPE:BOOL=TRUE" | |
259 | "-DVTK_USE_SYSTEM_HDF5:BOOL=TRUE" | |
260 | "-DVTK_USE_SYSTEM_JPEG:BOOL=TRUE" | |
261 | "-DVTK_USE_SYSTEM_JSONCPP:BOOL=TRUE" | |
262 | "-DVTK_USE_SYSTEM_LIBXML2:BOOL=TRUE" | |
263 | "-DVTK_USE_SYSTEM_OGGTHEORA:BOOL=TRUE" | |
264 | "-DVTK_USE_SYSTEM_PNG:BOOL=TRUE" | |
265 | "-DVTK_USE_SYSTEM_TIFF:BOOL=TRUE" | |
266 | "-DVTK_USE_SYSTEM_ZLIB:BOOL=TRUE") | |
267 | #:tests? #f)) ;XXX: no "test" target | |
268 | (inputs | |
269 | `(("libXt" ,libxt) | |
6a6db57f | 270 | ("xorgproto" ,xorgproto) |
fb226b43 JD |
271 | ("libX11" ,libx11) |
272 | ("libxml2" ,libxml2) | |
273 | ("mesa" ,mesa) | |
274 | ("glu" ,glu) | |
275 | ("expat" ,expat) | |
276 | ("freetype" ,freetype) | |
277 | ("hdf5" ,hdf5) | |
4bd428a7 | 278 | ("jpeg" ,libjpeg-turbo) |
fb226b43 JD |
279 | ("jsoncpp" ,jsoncpp) |
280 | ("libogg" ,libogg) | |
281 | ("libtheora" ,libtheora) | |
282 | ("png" ,libpng) | |
283 | ("tiff" ,libtiff) | |
284 | ("zlib" ,zlib))) | |
f1d4f264 | 285 | (home-page "https://vtk.org/") |
fb226b43 JD |
286 | (synopsis "Libraries for 3D computer graphics") |
287 | (description | |
288 | "The Visualization Toolkit (VTK) is a C++ library for 3D computer graphics, | |
289 | image processing and visualization. It supports a wide variety of | |
290 | visualization algorithms including: scalar, vector, tensor, texture, and | |
291 | volumetric methods; and advanced modeling techniques such as: implicit | |
292 | modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay | |
293 | triangulation. VTK has an extensive information visualization framework, has | |
294 | a suite of 3D interaction widgets, supports parallel processing, and | |
295 | integrates with various databases on GUI toolkits such as Qt and Tk.") | |
296 | (license license:bsd-3))) | |
62834314 | 297 | |
18696f7a RW |
298 | ;; itksnap needs an older variant of VTK. |
299 | (define-public vtk-6 | |
300 | (package (inherit vtk) | |
301 | (version "6.3.0") | |
302 | (source (origin | |
303 | (method url-fetch) | |
304 | (uri (string-append "https://vtk.org/files/release/" | |
305 | (version-major+minor version) | |
306 | "/VTK-" version ".tar.gz")) | |
307 | (sha256 | |
308 | (base32 | |
309 | "0pla1r5mvkgl4sl213gfdhzrypdgai0h3z5mfgm6p9jz9hsr794j")))) | |
310 | (inputs | |
311 | `(("jsoncpp" ,jsoncpp-for-tensorflow) | |
312 | ,@(alist-delete "jsoncpp" (package-inputs vtk)))))) | |
313 | ||
62834314 BH |
314 | (define-public opencv |
315 | (package | |
316 | (name "opencv") | |
63856931 | 317 | (version "3.4.3") |
62834314 | 318 | (source (origin |
6c56e9c4 EF |
319 | (method git-fetch) |
320 | (uri (git-reference | |
321 | (url "https://github.com/opencv/opencv") | |
322 | (commit version))) | |
323 | (file-name (git-file-name name version)) | |
62834314 BH |
324 | (sha256 |
325 | (base32 | |
6c56e9c4 | 326 | "06bc61r8myym4s8im10brdjfg4wxkrvsbhhl7vr1msdan2xddzi3")) |
8bf70426 TGR |
327 | (patches |
328 | (search-patches "opencv-fix-build-of-grfmt_jpeg2000.cpp.patch")) | |
62834314 BH |
329 | (modules '((guix build utils))) |
330 | (snippet | |
331 | '(begin | |
332 | ;; Remove external libraries. We have all available in Guix: | |
333 | (delete-file-recursively "3rdparty") | |
334 | ||
335 | ;; Milky icon set is non-free: | |
336 | (delete-file-recursively "modules/highgui/src/files_Qt/Milky") | |
337 | ||
338 | ;; Some jars found: | |
339 | (for-each delete-file | |
340 | '("modules/java/test/pure_test/lib/junit-4.11.jar" | |
6c56e9c4 EF |
341 | "samples/java/sbt/sbt/sbt-launch.jar")) |
342 | #t)))) | |
62834314 BH |
343 | (build-system cmake-build-system) |
344 | (arguments | |
345 | `(#:configure-flags | |
346 | (list "-DWITH_IPP=OFF" | |
347 | "-DWITH_ITT=OFF" | |
6949f45c | 348 | "-DWITH_CAROTENE=OFF" ; only visible on arm/aarch64 |
fdeb2def | 349 | "-DENABLE_PRECOMPILED_HEADERS=OFF" |
62834314 BH |
350 | |
351 | ;; CPU-Features: | |
352 | ;; See cmake/OpenCVCompilerOptimizations.cmake | |
353 | ;; (CPU_ALL_OPTIMIZATIONS) for a list of all optimizations | |
354 | ;; BASELINE is the minimum optimization all CPUs must support | |
355 | ;; | |
ebe0271a EF |
356 | ;; DISPATCH is the list of optional dispatches. |
357 | "-DCPU_BASELINE=SSE2" | |
62834314 | 358 | |
ebe0271a EF |
359 | ,@(match (%current-system) |
360 | ("x86_64-linux" | |
361 | '("-DCPU_DISPATCH=NEON;VFPV3;FP16;SSE;SSE2;SSE3;SSSE3;SSE4_1;SSE4_2;POPCNT;AVX;FP16;AVX2;FMA3;AVX_512F;AVX512_SKX" | |
362 | "-DCPU_DISPATCH_REQUIRE=SSE3,SSSE3,SSE4_1,SSE4_2,AVX,AVX2")) | |
363 | ("armhf-linux" | |
364 | '("-DCPU_BASELINE_DISABLE=NEON")) ; causes build failures | |
365 | ("aarch64-linux" | |
366 | '("-DCPU_BASELINE=NEON" | |
367 | "-DCPU_DISPATCH=NEON;VFPV3;FP16")) | |
368 | (_ '())) | |
62834314 BH |
369 | |
370 | "-DBUILD_PERF_TESTS=OFF" | |
6949f45c | 371 | "-DBUILD_TESTS=ON" |
62834314 | 372 | |
b5baf952 | 373 | (string-append "-DOPENCV_EXTRA_MODULES_PATH=" (getcwd) |
6c56e9c4 | 374 | "/opencv-contrib/modules") |
62834314 BH |
375 | |
376 | ;;Define test data: | |
b5baf952 | 377 | (string-append "-DOPENCV_TEST_DATA_PATH=" (getcwd) |
6c56e9c4 | 378 | "/opencv-extra/testdata") |
62834314 BH |
379 | |
380 | ;; Is ON by default and would try to rebuild 3rd-party protobuf, | |
381 | ;; which we had removed, which would lead to an error: | |
382 | "-DBUILD_PROTOBUF=OFF" | |
383 | ||
384 | ;; Rebuild protobuf files, because we have a slightly different | |
385 | ;; version than the included one. If we would not update, we | |
386 | ;; would get a compile error later: | |
387 | "-DPROTOBUF_UPDATE_FILES=ON" | |
388 | ||
389 | ;; xfeatures2d disabled, because it downloads extra binaries from | |
390 | ;; https://github.com/opencv/opencv_3rdparty | |
391 | ;; defined in xfeatures2d/cmake/download_{vgg|bootdesc}.cmake | |
392 | ;; Cmp this bug entry: | |
393 | ;; https://github.com/opencv/opencv_contrib/issues/1131 | |
394 | "-DBUILD_opencv_xfeatures2d=OFF") | |
395 | #:phases | |
396 | (modify-phases %standard-phases | |
397 | (add-after 'unpack 'disable-broken-tests | |
398 | (lambda _ | |
399 | ;; These tests fails with: | |
400 | ;; vtkXOpenGLRenderWindow (0x723990): Could not find a decent config | |
401 | ;; I think we have no OpenGL support with the Xvfb. | |
402 | (substitute* '("modules/viz/test/test_tutorial3.cpp" | |
403 | "modules/viz/test/test_main.cpp" | |
404 | "modules/viz/test/tests_simple.cpp" | |
405 | "modules/viz/test/test_viz3d.cpp") | |
406 | (("(TEST\\(Viz, )([a-z].*\\).*)" all pre post) | |
407 | (string-append pre "DISABLED_" post))) | |
408 | ||
409 | ;; This one fails with "unknown file: Failure" | |
410 | ;; But I couldn't figure out which file was missing: | |
6c56e9c4 | 411 | (substitute* "../opencv-contrib/modules/face/test/test_face_align.cpp" |
62834314 BH |
412 | (("(TEST\\(CV_Face_FacemarkKazemi, )(can_detect_landmarks\\).*)" |
413 | all pre post) | |
414 | (string-append pre "DISABLED_" post))) | |
415 | ||
416 | ;; Failure reason: Bad accuracy | |
417 | ;; Incorrect count of accurate poses [2nd case]: 90.000000 / 94.000000 | |
6c56e9c4 | 418 | (substitute* "../opencv-contrib/modules/rgbd/test/test_odometry.cpp" |
62834314 BH |
419 | (("(TEST\\(RGBD_Odometry_Rgbd, )(algorithmic\\).*)" all pre post) |
420 | (string-append pre "DISABLED_" post))) | |
421 | #t)) | |
422 | ||
62834314 BH |
423 | (add-after 'unpack 'unpack-submodule-sources |
424 | (lambda* (#:key inputs #:allow-other-keys) | |
425 | (mkdir "../opencv-extra") | |
426 | (mkdir "../opencv-contrib") | |
6c56e9c4 EF |
427 | (copy-recursively (assoc-ref inputs "opencv-extra") |
428 | "../opencv-extra") | |
429 | (invoke "tar" "xvf" | |
430 | (assoc-ref inputs "opencv-contrib") | |
431 | "--strip-components=1" | |
432 | "-C" "../opencv-contrib"))) | |
62834314 BH |
433 | |
434 | (add-after 'set-paths 'add-ilmbase-include-path | |
435 | (lambda* (#:key inputs #:allow-other-keys) | |
436 | ;; OpenEXR propagates ilmbase, but its include files do not appear | |
437 | ;; in the CPATH, so we need to add "$ilmbase/include/OpenEXR/" to | |
438 | ;; the CPATH to satisfy the dependency on "ImathVec.h". | |
439 | (setenv "CPATH" | |
440 | (string-append (assoc-ref inputs "ilmbase") | |
441 | "/include/OpenEXR" | |
442 | ":" (or (getenv "CPATH") ""))) | |
443 | #t)) | |
444 | (add-before 'check 'start-xserver | |
445 | (lambda* (#:key inputs #:allow-other-keys) | |
446 | (let ((xorg-server (assoc-ref inputs "xorg-server")) | |
447 | (disp ":1")) | |
448 | (setenv "HOME" (getcwd)) | |
449 | (setenv "DISPLAY" disp) | |
450 | ;; There must be a running X server and make check doesn't start one. | |
451 | ;; Therefore we must do it. | |
452 | (zero? (system (format #f "~a/bin/Xvfb ~a &" xorg-server disp))))))))) | |
453 | (native-inputs | |
6c56e9c4 | 454 | `(("pkg-config" ,pkg-config) |
ff337525 | 455 | ("xorg-server" ,xorg-server-for-tests) ; For running the tests |
62834314 BH |
456 | ("opencv-extra" |
457 | ,(origin | |
6c56e9c4 EF |
458 | (method git-fetch) |
459 | (uri (git-reference | |
460 | (url "https://github.com/opencv/opencv_extra") | |
461 | (commit version))) | |
462 | (file-name (git-file-name "opencv_extra" version)) | |
62834314 | 463 | (sha256 |
6c56e9c4 | 464 | (base32 "08p5xnq8n1jw8svvz0fnirfg7q8dm3p4a5dl7527s5xj0f9qn7lp")))) |
62834314 BH |
465 | ("opencv-contrib" |
466 | ,(origin | |
6c56e9c4 EF |
467 | (method git-fetch) |
468 | (uri (git-reference | |
469 | (url "https://github.com/opencv/opencv_contrib") | |
470 | (commit version))) | |
471 | (file-name (git-file-name "opencv_contrib" version)) | |
8e21fa0b | 472 | (patches (search-patches "opencv-rgbd-aarch64-test-fix.patch")) |
62834314 | 473 | (sha256 |
6c56e9c4 | 474 | (base32 "1f334glf39nk42mpqq6j732h3ql2mpz89jd4mcl678s8n73nfjh2")))))) |
4bd428a7 | 475 | (inputs `(("libjpeg" ,libjpeg-turbo) |
62834314 BH |
476 | ("libpng" ,libpng) |
477 | ("jasper" ,jasper) | |
478 | ;; ffmpeg 4.0 causes core dumps in tests. | |
479 | ("ffmpeg" ,ffmpeg-3.4) | |
480 | ("libtiff" ,libtiff) | |
481 | ("hdf5" ,hdf5) | |
482 | ("libgphoto2" ,libgphoto2) | |
483 | ("libwebp" ,libwebp) | |
484 | ("zlib" ,zlib) | |
485 | ("gtkglext" ,gtkglext) | |
486 | ("openexr" ,openexr) | |
487 | ("ilmbase" ,ilmbase) | |
488 | ("gtk+" ,gtk+-2) | |
489 | ("python-numpy" ,python-numpy) | |
490 | ("protobuf" ,protobuf) | |
491 | ("vtk" ,vtk) | |
492 | ("python" ,python))) | |
5834e4b7 BH |
493 | ;; These three CVEs are not a problem of OpenCV, see: |
494 | ;; https://github.com/opencv/opencv/issues/10998 | |
495 | (properties '((lint-hidden-cve . ("CVE-2018-7712" | |
496 | "CVE-2018-7713" | |
497 | "CVE-2018-7714")))) | |
62834314 BH |
498 | (synopsis "Computer vision library") |
499 | (description "OpenCV is a library aimed at | |
500 | real-time computer vision, including several hundred computer | |
501 | vision algorithms. It can be used to do things like: | |
502 | ||
503 | @itemize | |
504 | @item image and video input and output | |
505 | @item image and video processing | |
506 | @item displaying | |
507 | @item feature recognition | |
508 | @item segmentation | |
509 | @item facial recognition | |
510 | @item stereo vision | |
511 | @item structure from motion | |
512 | @item augmented reality | |
513 | @item machine learning | |
514 | @end itemize\n") | |
515 | (home-page "https://opencv.org/") | |
516 | (license license:bsd-3))) | |
5bbd6931 L |
517 | |
518 | (define-public vips | |
519 | (package | |
520 | (name "vips") | |
7e52321f TGR |
521 | (version "8.7.4") |
522 | (source | |
523 | (origin | |
524 | (method url-fetch) | |
525 | (uri (string-append | |
526 | "https://github.com/libvips/libvips/releases/download/v" | |
527 | version "/vips-" version ".tar.gz")) | |
528 | (sha256 | |
529 | (base32 "01gjhcrl6zj7mcj1al717v5jsniahplqhz1xkfh2j78vyfl1hxff")))) | |
5bbd6931 L |
530 | (build-system gnu-build-system) |
531 | (native-inputs | |
532 | `(("pkg-config" ,pkg-config) | |
533 | ("gobject-introspection" ,gobject-introspection))) | |
534 | (inputs | |
535 | `(("glib" ,glib) | |
4bd428a7 | 536 | ("libjpeg" ,libjpeg-turbo) |
5bbd6931 L |
537 | ("libpng" ,libpng) |
538 | ("librsvg" ,librsvg) | |
539 | ("libtiff" ,libtiff) | |
540 | ("libexif" ,libexif) | |
541 | ("giflib" ,giflib) | |
542 | ("libgsf" ,libgsf) | |
543 | ("fftw" ,fftw) | |
544 | ("poppler" ,poppler) | |
545 | ("pango" ,pango) | |
546 | ("lcms" ,lcms) | |
547 | ("matio" ,matio) | |
548 | ("libwebp" ,libwebp) | |
549 | ("niftilib" ,niftilib) | |
550 | ("openexr" ,openexr) | |
551 | ("orc" ,orc) | |
552 | ("imagemagick" ,imagemagick) | |
553 | ("libxml2" ,libxml2) | |
554 | ("expat" ,expat) | |
555 | ("hdf5" ,hdf5))) | |
556 | (home-page "https://libvips.github.io/libvips/") | |
85e2f212 | 557 | (synopsis "Multithreaded image processing system with low memory needs") |
37c1cf89 | 558 | (description |
85e2f212 TGR |
559 | "VIPS is a demand-driven, horizontally threaded image processing library. |
560 | It's particularly good at processing large images, working with colour, | |
561 | scientific analysis, and general research & development. | |
562 | ||
563 | Compared to most image processing libraries VIPS needs little RAM and runs | |
564 | quickly, especially on machines with more than one CPU core. This is primarily | |
565 | due to its architecture which automatically parallelises the image workflows.") | |
5bbd6931 | 566 | (license license:lgpl2.1+))) |
e506b5e9 | 567 | |
657f8535 VM |
568 | (define-public gmic |
569 | (package | |
570 | (name "gmic") | |
84479dcc | 571 | (version "2.9.2") |
657f8535 VM |
572 | (source |
573 | (origin | |
574 | (method url-fetch) | |
575 | (uri (string-append "https://gmic.eu/files/source/gmic_" | |
576 | version ".tar.gz")) | |
577 | (sha256 | |
84479dcc | 578 | (base32 "14acph914a8lp6qqfmp319ggqjg3i3hmalmnpk3mp07m7vpv2p9q")))) |
657f8535 VM |
579 | (build-system cmake-build-system) |
580 | (arguments | |
581 | `(#:tests? #f)) ;there are no tests | |
582 | (native-inputs | |
583 | `(("pkg-config" ,pkg-config))) | |
584 | (inputs | |
585 | `(("curl" ,curl) | |
586 | ("fftw" ,fftw) | |
587 | ("graphicsmagick" ,graphicsmagick) | |
588 | ("libjpeg-turbo" ,libjpeg-turbo) | |
589 | ("libpng" ,libpng) | |
590 | ("libtiff" ,libtiff) | |
591 | ("libx11" ,libx11) | |
592 | ;;("opencv" ,opencv) ;OpenCV is currently broken in the CI | |
593 | ("openexr" ,openexr) | |
594 | ("zlib" ,zlib))) | |
595 | (home-page "https://gmic.eu/") | |
596 | (synopsis "Full-featured framework for digital image processing") | |
597 | (description "G'MIC is a full-featured framework for digital image | |
598 | processing. It provides several user interfaces to convert / manipulate | |
599 | / filter / visualize generic image datasets, ranging from 1D scalar | |
600 | signals to 3D+t sequences of multi-spectral volumetric images, hence | |
601 | including 2D color images.") | |
602 | ;; Dual-licensed, either license applies. | |
603 | (license (list license:cecill license:cecill-c)))) | |
604 | ||
e506b5e9 L |
605 | (define-public nip2 |
606 | (package | |
607 | (name "nip2") | |
f2d3d742 | 608 | (version "8.7.1") |
e506b5e9 L |
609 | (source |
610 | (origin | |
611 | (method url-fetch) | |
612 | (uri (string-append "https://github.com/libvips/nip2/releases/download/v" | |
613 | version "/nip2-" version ".tar.gz" )) | |
614 | (sha256 | |
f2d3d742 | 615 | (base32 "0l7n427njif53npqn02gfjjly8y3khbrkzqxp10j5vp9h97psgiw")))) |
e506b5e9 L |
616 | (build-system gnu-build-system) |
617 | (arguments | |
618 | `(#:phases | |
619 | (modify-phases %standard-phases | |
f2d3d742 | 620 | ;; test_conv.ws keep failing so disabling for now. |
e506b5e9 L |
621 | (add-after 'unpack 'disable-test-conv |
622 | (lambda _ | |
623 | (delete-file "test/workspaces/test_conv.ws") | |
624 | #t)) | |
625 | (add-before 'check 'set-home | |
626 | (lambda _ | |
627 | (setenv "HOME" "/tmp") #t))))) | |
628 | (inputs | |
629 | `(("vips" ,vips) | |
630 | ("glib" ,glib) | |
631 | ("libtiff" ,libtiff) | |
632 | ("gtk+-2" ,gtk+-2) | |
633 | ("libxml2" ,libxml2) | |
634 | ("libexif" ,libexif) | |
4bd428a7 | 635 | ("libjpeg" ,libjpeg-turbo) ;required by vips.pc |
e506b5e9 L |
636 | ("librsvg" ,librsvg) |
637 | ("fftw" ,fftw) | |
638 | ("libgsf" ,libgsf) | |
639 | ("imagemagick" ,imagemagick) | |
640 | ("orc" ,orc) | |
641 | ("matio" ,matio) | |
642 | ("lcms" ,lcms) | |
643 | ("libwebp" ,libwebp) | |
644 | ("openexr" ,openexr) | |
645 | ("poppler" ,poppler) | |
646 | ("gsl" ,gsl))) | |
647 | (native-inputs | |
648 | `(("flex" ,flex) | |
649 | ("bison" ,bison) | |
650 | ("pkg-config" ,pkg-config))) | |
651 | (home-page "https://github.com/libvips/nip2") | |
652 | (synopsis "Spreadsheet-like GUI for libvips") | |
653 | (description "This package provide a graphical user interface (GUI) for | |
654 | the VIPS image processing library. It's a little like a spreadsheet: you | |
655 | create a set of formula connecting your objects together, and on a change nip2 | |
656 | recalculates.") | |
657 | (license license:gpl2+))) | |
02e1acfb RW |
658 | |
659 | (define-public vxl | |
660 | (package | |
661 | (name "vxl") | |
662 | (version "2.0.2") | |
663 | (source | |
664 | (origin | |
665 | (method git-fetch) | |
666 | (uri (git-reference | |
b0e7b699 | 667 | (url "https://github.com/vxl/vxl") |
02e1acfb RW |
668 | (commit (string-append "v" version)))) |
669 | (file-name (git-file-name name version)) | |
670 | (sha256 | |
671 | (base32 "0949hw57szq8943f1whwqaz591xjmb19kj803hcv74hdai2b0ycg")) | |
672 | (modules '((guix build utils))) | |
673 | ;; TODO: vxl includes an old version of dcmtk. It won't build with | |
674 | ;; version 3.6.x. | |
675 | (snippet | |
676 | '(begin | |
677 | (for-each delete-file-recursively | |
678 | '("v3p/bzlib/" | |
679 | "v3p/geotiff/" | |
680 | "v3p/jpeg/" | |
681 | "v3p/png/" | |
682 | "v3p/tiff/" | |
683 | "v3p/zlib/")) | |
684 | (substitute* "v3p/CMakeLists.txt" | |
685 | (("add_subdirectory\\((tiff|png|jpeg|zlib|bzlib|geotiff)\\)") | |
686 | "")) | |
687 | #t)))) | |
688 | (build-system cmake-build-system) | |
689 | (inputs | |
690 | `(("libgeotiff" ,libgeotiff) | |
691 | ("libtiff" ,libtiff) | |
4bd428a7 | 692 | ("libjpeg" ,libjpeg-turbo) |
02e1acfb RW |
693 | ("libpng" ,libpng) |
694 | ("zlib" ,zlib))) | |
695 | (home-page "https://github.com/vxl/vxl/") | |
696 | (synopsis "Collection of C++ libraries for computer vision") | |
697 | (description "VXL (the Vision-something-Libraries) is a collection of C++ | |
698 | libraries designed for computer vision research and implementation.") | |
699 | (license license:bsd-3))) | |
4243af4e RW |
700 | |
701 | (define-public vxl-1 | |
702 | (package (inherit vxl) | |
703 | (name "vxl") | |
704 | (version "1.18.0") | |
705 | (source | |
706 | (origin | |
707 | (method git-fetch) | |
708 | (uri (git-reference | |
b0e7b699 | 709 | (url "https://github.com/vxl/vxl") |
4243af4e RW |
710 | (commit (string-append "v" version)))) |
711 | (file-name (git-file-name name version)) | |
712 | (sha256 | |
713 | (base32 "1g4mr2cc58jwm0vasscbd4y5380wj3ahkvq121z4gs83fhavvxgz")) | |
714 | (modules '((guix build utils))) | |
715 | (snippet | |
716 | '(begin | |
717 | (for-each delete-file-recursively | |
718 | '("v3p/bzlib/" | |
719 | "v3p/geotiff/" | |
720 | "v3p/png/" | |
721 | "v3p/tiff/" | |
722 | "v3p/zlib/")) | |
723 | (substitute* "v3p/CMakeLists.txt" | |
724 | (("add_subdirectory\\((tiff|png|jpeg|zlib|bzlib|geotiff)\\)") | |
725 | "")) | |
726 | #t)))) | |
727 | (arguments | |
728 | `(#:configure-flags | |
729 | ;; Needed for itk-snap | |
730 | (list "-DVNL_CONFIG_LEGACY_METHODS=ON"))))) | |
d7701e1b RW |
731 | |
732 | (define-public insight-toolkit | |
733 | (package | |
734 | (name "insight-toolkit") | |
735 | (version "5.0.0") | |
736 | (source | |
737 | (origin | |
738 | (method url-fetch) | |
739 | (uri (string-append "https://github.com/InsightSoftwareConsortium/ITK/" | |
740 | "releases/download/v" version "/InsightToolkit-" | |
741 | version ".tar.xz")) | |
742 | (sha256 | |
743 | (base32 "0bs63mk4q8jmx38f031jy5w5n9yy5ng9x8ijwinvjyvas8cichqi")))) | |
744 | (build-system cmake-build-system) | |
745 | (arguments | |
746 | `(#:tests? #f ; tests require network access and external data | |
747 | #:configure-flags | |
748 | '("-DITK_USE_GPU=ON" | |
749 | "-DITK_USE_SYSTEM_LIBRARIES=ON" | |
750 | "-DITK_USE_SYSTEM_GOOGLETEST=ON" | |
751 | "-DITK_BUILD_SHARED=ON" | |
752 | ;; This prevents "GTest::GTest" from being added to the ITK_LIBRARIES | |
753 | ;; variable in the installed CMake files. This is necessary as other | |
754 | ;; packages using insight-toolkit could not be configured otherwise. | |
755 | "-DGTEST_ROOT=gtest") | |
756 | #:phases | |
757 | (modify-phases %standard-phases | |
758 | (add-after 'unpack 'do-not-tune | |
759 | (lambda _ | |
760 | (substitute* "CMake/ITKSetStandardCompilerFlags.cmake" | |
761 | (("-mute=native") "")) | |
762 | #t))))) | |
763 | (inputs | |
764 | `(("eigen" ,eigen) | |
765 | ("expat" ,expat) | |
766 | ("fftw" ,fftw) | |
767 | ("fftwf" ,fftwf) | |
768 | ("hdf5" ,hdf5) | |
4bd428a7 | 769 | ("libjpeg" ,libjpeg-turbo) |
d7701e1b RW |
770 | ("libpng" ,libpng) |
771 | ("libtiff" ,libtiff) | |
772 | ("mesa" ,mesa-opencl) | |
773 | ("perl" ,perl) | |
774 | ("python" ,python) | |
775 | ("tbb" ,tbb) | |
776 | ("vxl" ,vxl-1) | |
777 | ("zlib" ,zlib))) | |
778 | (native-inputs | |
779 | `(("googletest" ,googletest) | |
780 | ("pkg-config" ,pkg-config))) | |
781 | (home-page "https://github.com/InsightSoftwareConsortium/ITK/") | |
782 | (synopsis "Scientific image processing, segmentation and registration") | |
783 | (description "The Insight Toolkit (ITK) is a toolkit for N-dimensional | |
784 | scientific image processing, segmentation, and registration. Segmentation is | |
785 | the process of identifying and classifying data found in a digitally sampled | |
786 | representation. Typically the sampled representation is an image acquired | |
787 | from such medical instrumentation as CT or MRI scanners. Registration is the | |
788 | task of aligning or developing correspondences between data. For example, in | |
789 | the medical environment, a CT scan may be aligned with a MRI scan in order to | |
790 | combine the information contained in both.") | |
791 | (license license:asl2.0))) | |
8f4d457d RW |
792 | |
793 | (define-public insight-toolkit-4 | |
794 | (package (inherit insight-toolkit) | |
795 | (version "4.13.2") | |
796 | (source | |
797 | (origin | |
798 | (method url-fetch) | |
799 | (uri (string-append "https://github.com/InsightSoftwareConsortium/ITK/" | |
800 | "releases/download/v" version "/InsightToolkit-" | |
801 | version ".tar.xz")) | |
802 | (sha256 | |
803 | (base32 "19cgfpd63gqrvc3m27m394gy2d7w79g5y6lvznb5qqr49lihbgns")))) | |
804 | (arguments | |
805 | `(#:tests? #f ; tests require network access and external data | |
806 | #:configure-flags | |
807 | '("-DITKV3_COMPATIBILITY=ON" ; needed for itk-snap | |
808 | "-DITK_USE_GPU=ON" | |
809 | "-DITK_USE_SYSTEM_LIBRARIES=ON" | |
810 | "-DITK_USE_SYSTEM_GOOGLETEST=ON" | |
811 | "-DITK_USE_SYSTEM_VXL=ON"))))) | |
07f36b0c RW |
812 | |
813 | (define-public insight-toolkit-4.12 | |
814 | (package (inherit insight-toolkit-4) | |
815 | (version "4.12.2") | |
816 | (source | |
817 | (origin | |
818 | (method url-fetch) | |
819 | (uri (string-append "mirror://sourceforge/itk/itk/4.12/" | |
820 | "InsightToolkit-" version ".tar.xz")) | |
821 | (sha256 | |
822 | (base32 "1qw9mxbh083siljygahl4gdfv91xvfd8hfl7ghwii19f60xrvn2w")))))) | |
1c4e6aa9 RW |
823 | |
824 | (define-public itk-snap | |
825 | (package | |
826 | (name "itk-snap") | |
827 | (version "3.8.0") | |
828 | (source | |
829 | (origin | |
830 | (method git-fetch) | |
831 | (uri (git-reference | |
832 | (url "https://git.code.sf.net/p/itk-snap/src") | |
833 | (commit (string-append "v" version)))) | |
834 | (file-name (git-file-name name version)) | |
835 | (sha256 | |
836 | (base32 "15i5ixpryfrbf3vrrb5rici8fb585f25k0v1ljds16bp1f1msr4q")))) | |
837 | (build-system cmake-build-system) | |
838 | (arguments | |
839 | `(#:configure-flags | |
840 | (list "-DSNAP_VERSION_GIT_SHA1=release" | |
841 | "-DSNAP_VERSION_GIT_BRANCH=release" | |
842 | "-DSNAP_VERSION_GIT_TIMESTAMP=0" | |
843 | "-DSNAP_PACKAGE_QT_PLUGINS=OFF" | |
0fe041bd | 844 | "-DCMAKE_POSITION_INDEPENDENT_CODE=ON") |
1c4e6aa9 RW |
845 | #:phases |
846 | (modify-phases %standard-phases | |
847 | ;; During the installation phase all libraries provided by all | |
848 | ;; dependencies will be copied to the lib directory. That's insane, | |
849 | ;; so we disable this. | |
850 | (add-after 'unpack 'do-not-copy-dependencies | |
851 | (lambda _ | |
852 | (substitute* "CMakeLists.txt" | |
853 | (("install_qt5_executable\ | |
854 | \\(\\$\\{SNAP_MAIN_INSTALL_DIR\\}/\\$\\{SNAP_EXE\\}\\)") | |
855 | "")) | |
856 | #t)) | |
857 | (add-after 'unpack 'disable-gui-tests | |
858 | (lambda _ | |
859 | ;; The GUI tests just time out. | |
860 | (substitute* "CMakeLists.txt" | |
861 | ((" (Workspace|DiffSpace|ProbeIntensity|RegionCompetition\ | |
862 | |RandomForest|RandomForestBailOut)") | |
863 | "")) | |
864 | #t)) | |
865 | (add-after 'unpack 'make-reproducible | |
866 | (lambda _ | |
867 | (substitute* "CMakeLists.txt" | |
868 | (("TODAY\\(SNAP_VERSION_COMPILE_DATE\\)") | |
869 | "SET(SNAP_VERSION_COMPILE_DATE \"(removed for reproducibility)\")")) | |
870 | #t)) | |
871 | (add-after 'unpack 'prepare-submodules | |
872 | (lambda* (#:key inputs #:allow-other-keys) | |
873 | (rmdir "Submodules/c3d") | |
874 | (copy-recursively (assoc-ref inputs "c3d-src") | |
875 | "Submodules/c3d") | |
876 | (substitute* '("Submodules/c3d/adapters/BiasFieldCorrectionN4.cxx" | |
877 | "Submodules/c3d/adapters/ApplyMetric.cxx") | |
878 | (("vcl_") "std::")) | |
879 | (rmdir "Submodules/greedy") | |
880 | (symlink (assoc-ref inputs "greedy-src") | |
881 | "Submodules/greedy") | |
882 | #t)) | |
883 | (add-after 'unpack 'fix-includes | |
884 | (lambda _ | |
885 | (substitute* "GUI/Model/RegistrationModel.cxx" | |
886 | (("<vnl_symmetric_eigensystem.h>") | |
887 | "<vnl/algo/vnl_symmetric_eigensystem.h>")) | |
888 | #t)) | |
889 | (add-before 'check 'prepare-tests | |
890 | (lambda _ | |
891 | ;; Needed by at least one test. | |
892 | (setenv "HOME" "/tmp") | |
893 | #t)) | |
894 | (add-after 'install 'wrap-executable | |
895 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
896 | (let ((out (assoc-ref outputs "out"))) | |
897 | (wrap-program (string-append out "/bin/itksnap") | |
898 | `("QT_PLUGIN_PATH" ":" prefix | |
899 | ,(map (lambda (label) | |
900 | (string-append (assoc-ref inputs label) | |
901 | "/lib/qt5/plugins")) | |
902 | '("qtbase" "qtdeclarative")))) | |
903 | #t)))))) | |
904 | (inputs | |
905 | `(("curl" ,curl) | |
906 | ("fftw" ,fftw) | |
907 | ("fftwf" ,fftwf) | |
908 | ("glu" ,glu) | |
909 | ("hdf5" ,hdf5) | |
910 | ("mesa" ,mesa-opencl) | |
911 | ;; This package does not build with either insight-toolkit 5.0.0 and | |
912 | ;; not with 4.13. It really needs to be 4.12. | |
913 | ("itk" ,insight-toolkit-4.12) | |
914 | ("vtk" ,vtk-6) | |
915 | ("qtbase" ,qtbase) | |
916 | ("qtdeclarative" ,qtdeclarative) | |
1c4e6aa9 RW |
917 | ("vxl" ,vxl-1) |
918 | ("zlib" ,zlib))) | |
919 | (native-inputs | |
920 | `(("googletest" ,googletest) | |
957e0be3 | 921 | ("qttools" ,qttools) |
1c4e6aa9 RW |
922 | ("pkg-config" ,pkg-config) |
923 | ("c3d-src" | |
924 | ,(let* ((commit "f521358db26e00002c911cc47bf463b043942ad3") | |
925 | (revision "1") | |
926 | (version (git-version "0" revision commit))) | |
927 | (origin | |
928 | (method git-fetch) | |
929 | (uri (git-reference | |
b0e7b699 | 930 | (url "https://github.com/pyushkevich/c3d") |
1c4e6aa9 RW |
931 | (commit commit))) |
932 | (file-name (git-file-name "c3d" version)) | |
933 | (sha256 | |
934 | (base32 | |
935 | "0kyv3rxrxwr8c3sa9zv01lsnhk95b27gx1s870k3yi8qp52h7bx3"))))) | |
936 | ;; We are using an arbitrary commit from 2017 because the latest | |
937 | ;; version breaks the build... | |
938 | ("greedy-src" | |
939 | ,(let* ((commit "97e340f7e8e66597599144947775e6039e79a0d3") | |
940 | (revision "1") | |
941 | (version (git-version "0" revision commit))) | |
942 | (origin | |
943 | (method git-fetch) | |
944 | (uri (git-reference | |
b0e7b699 | 945 | (url "https://github.com/pyushkevich/greedy") |
1c4e6aa9 RW |
946 | (commit commit))) |
947 | (file-name (git-file-name "greedy" version)) | |
948 | (sha256 | |
949 | (base32 | |
950 | "0k5bc9za4jrc8z9dj08z1rkcp5xf0gnd1d2jmi1w9ny4vxh2q2ab"))))))) | |
951 | (home-page "https://sourceforge.net/p/itk-snap/") | |
952 | (synopsis "Medical image segmentation") | |
953 | (description "ITK-SNAP is a tool for segmenting anatomical structures in | |
954 | medical images. It provides an automatic active contour segmentation | |
955 | pipeline, along with supporting a manual segmentation toolbox. ITK-SNAP has a | |
956 | full-featured UI aimed at clinical researchers.") | |
957 | ;; This includes the submodules greedy and c3d. | |
958 | (license license:gpl3+))) | |
85c4f486 PN |
959 | |
960 | (define-public metapixel | |
961 | ;; Follow stable branch. | |
962 | (let ((commit "98ee9daa093b6c334941242e63f90b1c2876eb4f")) | |
963 | (package | |
964 | (name "metapixel") | |
965 | (version (git-version "1.0.2" "1" commit)) | |
966 | (source | |
967 | (origin | |
968 | (method git-fetch) | |
969 | (uri (git-reference | |
970 | (url "https://github.com/schani/metapixel") | |
971 | (commit commit) | |
972 | ;; TODO: Package rwimg and lispreader? | |
973 | (recursive? #t))) | |
974 | (file-name (git-file-name name version)) | |
975 | (sha256 | |
976 | (base32 "0r7n3a6bvcxkbpda4mwmrpicii09iql5z69nkjqygkwxw7ny3309")))) | |
977 | (build-system gnu-build-system) | |
978 | (inputs | |
979 | `(("giflib" ,giflib) | |
980 | ("libjpeg" ,libjpeg-turbo) | |
981 | ("libpng" ,libpng) | |
982 | ("perl" ,perl))) | |
983 | (native-inputs | |
984 | `(("pkg-config" ,pkg-config) | |
985 | ("docbook-xml" ,docbook-xml) | |
986 | ("docbook-xsl" ,docbook-xsl) | |
987 | ("xsltproc" ,libxslt))) | |
988 | (arguments | |
989 | `(#:tests? #f ; No tests. | |
990 | #:make-flags (list | |
991 | (string-append "PREFIX=" (assoc-ref %outputs "out")) | |
992 | (string-append "MANPAGE_XSL=" | |
993 | (assoc-ref %build-inputs "docbook-xsl") | |
994 | "/xml/xsl/docbook-xsl-*/manpages/docbook.xsl")) | |
995 | #:phases | |
996 | (modify-phases %standard-phases | |
997 | (delete 'configure) | |
998 | (add-before 'install 'make-local-docbook-xml | |
999 | (lambda* (#:key inputs #:allow-other-keys) | |
1000 | (substitute* "metapixel.xml" | |
1001 | (("http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd") | |
1002 | (string-append (assoc-ref inputs "docbook-xml") | |
1003 | "/xml/dtd/docbook/docbookx.dtd"))) | |
1004 | #t)) | |
1005 | (add-before 'install 'fix-directory-creation | |
1006 | (lambda* (#:key outputs #:allow-other-keys) | |
1007 | (mkdir-p (string-append (assoc-ref outputs "out") "/share/man/man1")) | |
1008 | #t))))) | |
1009 | (home-page "https://www.complang.tuwien.ac.at/schani/metapixel/") | |
1010 | (synopsis "Photomosaics generator") | |
1011 | (description "Metapixel is a program for generating photomosaics. It can | |
1012 | generate classical photomosaics, in which the source image is viewed as a | |
1013 | matrix of equally sized rectangles for each of which a matching image is | |
1b8be80e | 1014 | substituted, as well as collage-style photomosaics, in which rectangular parts |
85c4f486 PN |
1015 | of the source image at arbitrary positions (i.e. not aligned to a matrix) are |
1016 | substituted by matching images.") | |
1017 | (license license:gpl2)))) |