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