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