diff options
Diffstat (limited to 'sci-libs/itk')
20 files changed, 2008 insertions, 759 deletions
diff --git a/sci-libs/itk/Manifest b/sci-libs/itk/Manifest index cae86acd2..87328da27 100644 --- a/sci-libs/itk/Manifest +++ b/sci-libs/itk/Manifest @@ -1,5 +1,12 @@ -DIST DoxygenInsightToolkit-4.4.0.tar.gz 779393284 SHA256 a2e9a74dad840f6af7e3f3a518f43d75cad511d6b6b4b09d61f5b1b1b72d25c3 SHA512 9bdd6cedcdf5c30afb7f73130074983a56c397db776b927aae78b15a80d1158cca4563f92795d804ade34f4860b350cbbd157ed6924d53cb2ddfccf478e403c6 WHIRLPOOL 114f6ebb4052a8845559a9fa7f2883aa7bba90ff07dd7cd64d4e305e5ffdb35969b8b18b31b631e99d293fe06d95389359b23697544797a7703d9a973bd23246 -DIST DoxygenInsightToolkit-4.5.0.tar.gz 871324021 SHA256 bcc66662aa836cbb287a184870ba0aaf1b94e47d16d8e5d8bd2d30d77172781e SHA512 0bdf870c1600d847a635eefb8109dc12030387124de70c5c2b03f6a61bab796ce39c56792fcaa5779f741fce9c4d9bc621dcd70b389a805301e14c01422202a1 WHIRLPOOL 6315d22958bbfd7435d9948f1da6f3c1695abf441fc80b6c3545ad48cff42c4c0e871c091251c40cc7a2db422123304d4feaf08527c67236b34ced11c569487d -DIST InsightToolkit-4.12.0.tar.xz 12246508 BLAKE2B c14cf0b4b1fab8a6f27f1e863ff79228473dd1d9c7fe76bca3791d8c3fad39a4f448ee81cee9ca52a974df166db7b22cd6896353482bf8c587c272266501ea5a SHA512 b0ed1a9e02d238783edf68706ae9bdd23d2cf3e90274caa0f09faafab2d55729663a45f4ef4f5884f07a2160c5dcfb179ec445718b83e235007a0002a7e19e96 -DIST InsightToolkit-4.4.2.tar.gz 231905134 BLAKE2B 910c08916b3c22f0245aed39378c8f73191d57294032c9fafae1dbe168644312921512e9520c96ba7ed409c20631f9d6a9d71241162cbb868cba4638614b7a04 SHA512 c65beca4dd60aa769871bb3089cbb421729a2dcbd8bd3ec42c378ed60828e4327f1faf062f77bcca34306315a1daee6bc29d858dab9aea1c08f4843405fd21e3 -DIST InsightToolkit-4.5.1.tar.xz 212785824 BLAKE2B 1586da2a7d4ff2c65d70459b7f6ddd9dcd04facb2c50fee6b11b6ab78eb2b4bf26b1f4bcbf7c622d7dce098348b9e510bf6f3974a047a7ad9ba3ee58abf44e11 SHA512 a613d37236e3fad68bf83c023141cef72ebfd901ebe371157f474446e0b98fc291f8c5b82b7cb60f01868b78621b919d3602b3768272173e2fe3be96f0813dbb +DIST ITKAdaptiveDenoising-5.2.1.tar.gz 757851 BLAKE2B 3d94e1db6d2524adf7491e6e24308618b7b69e54184cbfe29a7084b55b8a337228a308233e0f0ab2cef04df9c8f42010a758e0071efdfd4905c28ca6399bfdfd SHA512 7e9c5a6681cd9777b33f11d1a1a5f6d8b1b6f7d2ec2d4d829398c78045b53b247bddea99e4a5450ba8d6666a31b5216ef6e07a2c874c5723af072e0d3c8cf9f4 +DIST ITKAdaptiveDenoising-5.3.0.tar.gz 757851 BLAKE2B 3d94e1db6d2524adf7491e6e24308618b7b69e54184cbfe29a7084b55b8a337228a308233e0f0ab2cef04df9c8f42010a758e0071efdfd4905c28ca6399bfdfd SHA512 7e9c5a6681cd9777b33f11d1a1a5f6d8b1b6f7d2ec2d4d829398c78045b53b247bddea99e4a5450ba8d6666a31b5216ef6e07a2c874c5723af072e0d3c8cf9f4 +DIST ITKGenericLabelInterpolator-1.2.0.tar.gz 137697 BLAKE2B f7bb877654e852f56f8eb1086f988ec3b71106b6528d5cf03734a3c3eb4ce5ac875b52081e0a1339ac237e1616b0516b8cc8efb4429ec0e5ef64ac5461a40836 SHA512 bc1fcd3c13cb182420bb4a5d2c9c789553f8b7b581fd7d0b7d687331e22c90d30efdd338bfbc22dfb8c97d3ab7209f761425c4d12755655d86d81ffb231d881c +DIST ITKGenericLabelInterpolator-5.2.1.tar.gz 140427 BLAKE2B b19703872926516d9d07acd4078d343e02f00a162d2cb8b6787d6210223be375a059e767cf9c32dd234e77ff51d1af5e08d9a9844c34e23a531938c7d3ded4a9 SHA512 69e53b281cd3f7c136ad9e7ded2c362e0d9e22dc2bd595f42abcefe2cf9ec4fa0f44192efc3d328290be4adaee1ebd74be3035b18147081cc8b8479a333cdea6 +DIST InsightData-5.2.1.tar.gz 293448802 BLAKE2B fd2bb012c0d96243d3543993a87e73c43be0626b0478959e36633f22c7e8d48a46d0f4d18fa3a8d952d4a705ca20594d92c07044000b8e1bc65390ce981af3e7 SHA512 93eae6bdf62ce29ea6dfb1dddedffe4046400a86074dd4d47e3ddcd7ff9ab10031363275cb7f9741add7c02343f1f3e6a41b0ec6533531f4a3a42607c51aa704 +DIST InsightData-5.3.0.tar.gz 366826437 BLAKE2B ae3cbb3f7a51d6b86717a073c0eb55c528baeff240f44413c25ce11319a7e0ef9ff073d1cb94d2d15d104687fe5b8e95d0d4286832dbb02993da8fe706fecb28 SHA512 3caf7d1d64543312d668ef1a6b8c879161a37deee5c980fbfeb14e299a296a2825ae48463bff915f50c98ec0ccdbef3e1aff7c4f52604a93c6028951f90a4757 +DIST InsightToolkit-5.2.1.tar.gz 20702482 BLAKE2B 06dc73a80b4999baff3fc75e225c8720d00927fd268bd0398bb0eea44679777b777836f307f02a2df3641a300e17c9c2ee9f77d2a87539bf8a6ed49ce341bf23 SHA512 6786e39cdf3d0c3a31abd1e23481e30f6dc9dac189ffe372dde3db688f2f57686a8beb321778327e1ff683ed844d41f1dee937b0ba542b2365e2195dfca398c7 +DIST InsightToolkit-5.3.0.tar.gz 21577835 BLAKE2B 7538b673cbe17ab23d6b70e2cb2486e6711df6a79d6806c641a10a8b624c4723ca5f562b97be814551c79c42dea772ac64ed7bc8fdf2d28f5a95cb6462e50638 SHA512 29359839c0fb13acd430410e6adadbecb4d9d8cb4871a0aba0ac67b539c235354a591655dd654f43daa5f035a33721671d665eee8a4a129a9d0d3419e2356e97 +DIST itk-5.2.1-testingdata.tar.gz 2411475710 BLAKE2B edb8ba9bea8bf890749aa46ab3fb29f7d3e25e0f8bb7da7d7cca8c6524f75778b823232536602ade763c025b8e0fe134a555e6fcf652b8d42cc08f08cbd0c29b SHA512 89b160dc5f7781e148aad065f539b80b9accb9ec384e424398287e62b42a88cff610afcf41622a6d3e4e12c1938e7403b3dae65fa13bfb40c29a6b2f90a02398 +DIST itk-5.3.0-testingdata.tar.gz 2569680868 BLAKE2B a358bdb3a9f6de883e9fe41129af88d7a476acc4839fd17075d484a441db40d7f1f2f247d07701817464de5c997b18066628921652630a5f110e238d3f2419ec SHA512 5fa0834c25d128c915b5bdaefb13574952e680fe52a5c99ced614737e52f57abce59510be764766ce43769ae5731c35c7d646cdf3e21f495aee14fbb7d1835b4 +DIST itk-test-a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a 214819 BLAKE2B cd65212e72cb80eff54ee3f22d05b55036470684c582334fe94826a2d4ed49c840c50a214996f64f2bcd710e5973c2d46201ef31732fe847a43504379df62e25 SHA512 a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a +DIST itk-test-bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f 215417 BLAKE2B 318a6c55ba259a5af1e3e19cf859267caa0a612b05abfd9a83d9943902fd7edc25ec002707ed4ec85f7aebd4c5a82411942b5cfe2dc713c905a5bb5d1aa5ef23 SHA512 bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f diff --git a/sci-libs/itk/files/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch b/sci-libs/itk/files/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch deleted file mode 100644 index 094ee3229..000000000 --- a/sci-libs/itk/files/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch +++ /dev/null @@ -1,50 +0,0 @@ -From d069b7b94287dae15fcaf707775f5dd2bbebcc38 Mon Sep 17 00:00:00 2001 -From: Matt McCormick <matt.mccormick@kitware.com> -Date: Wed, 5 Feb 2014 15:52:34 -0500 -Subject: [PATCH 1/3] BUG: Wrap TransformFileReader, TransformFileWriter. - -Missing CMakeLists.txt in the wrapping directory. Need to explicitly include -the headers after "Template" was appended to the class name. - -Suggested-by: Sami Koho <sami.koho@gmail.com> - -Change-Id: I6f994bb18f37d5adf1d0f0311fa73506c41239a7 ---- - Modules/IO/TransformBase/wrapping/CMakeLists.txt | 3 +++ - Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap | 2 ++ - Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap | 2 ++ - 3 files changed, 7 insertions(+) - create mode 100644 Modules/IO/TransformBase/wrapping/CMakeLists.txt - -diff --git a/Modules/IO/TransformBase/wrapping/CMakeLists.txt b/Modules/IO/TransformBase/wrapping/CMakeLists.txt -new file mode 100644 -index 0000000..6072567 ---- /dev/null -+++ b/Modules/IO/TransformBase/wrapping/CMakeLists.txt -@@ -0,0 +1,3 @@ -+itk_wrap_module(ITKIOTransformBase) -+itk_auto_load_submodules() -+itk_end_wrap_module() -diff --git a/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap b/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap -index 9b52fbc..662df9e 100644 ---- a/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap -+++ b/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap -@@ -1,3 +1,5 @@ -+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF) -+itk_wrap_include("itkTransformFileReader.h") - itk_wrap_class("itk::TransformFileReaderTemplate" POINTER) - foreach(t ${WRAP_ITK_REAL}) - itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}") -diff --git a/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap b/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap -index 4f1ac4a..356aaf3 100644 ---- a/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap -+++ b/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap -@@ -1,3 +1,5 @@ -+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF) -+itk_wrap_include("itkTransformFileWriter.h") - itk_wrap_class("itk::TransformFileWriterTemplate" POINTER) - foreach(t ${WRAP_ITK_REAL}) - itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}") --- -1.8.5.3 - diff --git a/sci-libs/itk/files/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch b/sci-libs/itk/files/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch deleted file mode 100644 index 4c74d5451..000000000 --- a/sci-libs/itk/files/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch +++ /dev/null @@ -1,28 +0,0 @@ -From 66d2955fbe5528d9df216c639277d1d2686447e5 Mon Sep 17 00:00:00 2001 -From: Michka Popoff <michkapopoff@gmail.com> -Date: Fri, 7 Feb 2014 19:24:49 +0100 -Subject: [PATCH 2/3] COMP: Fixed itkQuasiNewtonOptimizerv4 wrapping warnings - -The warning : -/scratch/dashboards/Linux-x86_64-gcc4.4-WrapITK/ITK-build/Wrapping/Modules/ITKOptimizersv4/itkQuasiNewtonOptimizerv4.xml: warning(5): Unknown type type: itk::QuasiNewtonOptimizerv4 [typedef] -/scratch/dashboards/Linux-x86_64-gcc4.4-WrapITK/ITK-build/Wrapping/Modules/ITKOptimizersv4/itkQuasiNewtonOptimizerv4.xml: warning(4): ITK type not wrapped, or currently not known: itk::QuasiNewtonOptimizerv4Template< double > ---- - .../Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap | 8 +++++++- - 1 file changed, 7 insertions(+), 1 deletion(-) - -diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap -index 4a43dd4..7eed11c 100644 ---- a/Modules/Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap -+++ b/Modules/Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap -@@ -1 +1,7 @@ --itk_wrap_simple_class("itk::QuasiNewtonOptimizerv4" POINTER) -+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF) -+itk_wrap_include("itkQuasiNewtonOptimizerv4.h") -+itk_wrap_class("itk::QuasiNewtonOptimizerv4Template" POINTER) -+ foreach(t ${WRAP_ITK_REAL}) -+ itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}") -+ endforeach(t) -+itk_end_wrap_class() --- -1.8.5.3 - diff --git a/sci-libs/itk/files/0003-COMP-Fixed-itkGradientDescentOptimizerv4-wrapping-wa.patch b/sci-libs/itk/files/0003-COMP-Fixed-itkGradientDescentOptimizerv4-wrapping-wa.patch deleted file mode 100644 index d77345edf..000000000 --- a/sci-libs/itk/files/0003-COMP-Fixed-itkGradientDescentOptimizerv4-wrapping-wa.patch +++ /dev/null @@ -1,73 +0,0 @@ -From fced46ce8769b4edc7971ea0928045390b5c3f84 Mon Sep 17 00:00:00 2001 -From: Michka Popoff <michkapopoff@gmail.com> -Date: Mon, 10 Feb 2014 09:41:42 +0100 -Subject: [PATCH 3/3] COMP: Fixed itkGradientDescentOptimizerv4 wrapping - warnings - -I splitted the 3 wrapping calls in 3 separate files and fixed the wrapping. - -The warnings : -/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(5): Unknown type type: itk::GradientDescentOptimizerBasev4 [typedef] -/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(5): Unknown type type: itk::GradientDescentOptimizerv4 [typedef] -/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(5): Unknown type type: itk::ObjectToObjectOptimizerBase [typedef] -/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(4): ITK type not wrapped, or currently not known: itk::GradientDescentOptimizerBasev4Template< double > -/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(4): ITK type not wrapped, or currently not known: itk::GradientDescentOptimizerv4Template< double > -/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(4): ITK type not wrapped, or currently not known: itk::ObjectToObjectOptimizerBaseTemplate< double > - -Should also hopefully fix the new error on the dashboard I introduced by fixing the itkQuasiNewtonOptimizerv4 warnings (http://review.source.kitware.com/#/c/14317/) -/home/kevin/kitware/ITK_Build/Wrapping/Typedefs/itkQuasiNewtonOptimizerv4.i:87: Warning 401: Nothing known about base class 'itk::GradientDescentOptimizerv4Template< float >'. Ignored. -/home/kevin/kitware/ITK_Build/Wrapping/Typedefs/itkQuasiNewtonOptimizerv4.i:87: Warning 401: Maybe you forgot to instantiate 'itk::GradientDescentOptimizerv4Template< float >' using %template. - -Change-Id: I15b6af11690ed6efeaced68f73af5212ab5dc364 ---- - .../wrapping/itkGradientDescentOptimizerBasev4.wrap | 7 +++++++ - .../Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap | 10 +++++++--- - .../Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap | 7 +++++++ - 3 files changed, 21 insertions(+), 3 deletions(-) - create mode 100644 Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerBasev4.wrap - create mode 100644 Modules/Numerics/Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap - -diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerBasev4.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerBasev4.wrap -new file mode 100644 -index 0000000..74f5a6c ---- /dev/null -+++ b/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerBasev4.wrap -@@ -0,0 +1,7 @@ -+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF) -+itk_wrap_include("itkGradientDescentOptimizerBasev4.h") -+itk_wrap_class("itk::GradientDescentOptimizerBasev4Template" POINTER) -+ foreach(t ${WRAP_ITK_REAL}) -+ itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}") -+ endforeach(t) -+itk_end_wrap_class() -diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap -index d53a176..3236448 100644 ---- a/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap -+++ b/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap -@@ -1,3 +1,7 @@ --itk_wrap_simple_class("itk::ObjectToObjectOptimizerBase" POINTER) --itk_wrap_simple_class("itk::GradientDescentOptimizerBasev4" POINTER) --itk_wrap_simple_class("itk::GradientDescentOptimizerv4" POINTER) -+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF) -+itk_wrap_include("itkGradientDescentOptimizerv4.h") -+itk_wrap_class("itk::GradientDescentOptimizerv4Template" POINTER) -+ foreach(t ${WRAP_ITK_REAL}) -+ itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}") -+ endforeach(t) -+itk_end_wrap_class() -diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap -new file mode 100644 -index 0000000..61b2c44 ---- /dev/null -+++ b/Modules/Numerics/Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap -@@ -0,0 +1,7 @@ -+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF) -+itk_wrap_include("itkObjectToObjectOptimizerBase.h") -+itk_wrap_class("itk::ObjectToObjectOptimizerBaseTemplate" POINTER) -+ foreach(t ${WRAP_ITK_REAL}) -+ itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}") -+ endforeach(t) -+itk_end_wrap_class() --- -1.8.5.3 - diff --git a/sci-libs/itk/files/0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch b/sci-libs/itk/files/0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch deleted file mode 100644 index 83b395626..000000000 --- a/sci-libs/itk/files/0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch +++ /dev/null @@ -1,30 +0,0 @@ -Author: Matt McCormick <matt.mccormick@kitware.com> -Date: Thu Feb 6 10:26:49 2014 -0500 - - COMP: Wrap OptimizerParameterScalesEstimatorTemplate. - - The class name changed and it became templated. Fixes: - - /playpen/blowekamp/MacOSX-WrapITK/ITK-build/Wrapping/Modules/ITKOptimizersv4/itkOptimizerParameterScalesEstimator.xml: - warning(5): Unknown type type: itk::OptimizerParameterScalesEstimator - [typedef] - /playpen/blowekamp/MacOSX-WrapITK/ITK-build/Wrapping/Modules/ITKOptimizersv4/itkOptimizerParameterScalesEstimator.xml: - warning(4): ITK type not wrapped, or currently not known: - itk::OptimizerParameterScalesEstimatorTemplate< double > - - Change-Id: Ic6b4d6fba10d5d6c7b58de8d842bad6511e1ae7b - -diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkOptimizerParameterScalesEstimator.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkOptim -index efd6a8c..a647ee4 100644 ---- a/Modules/Numerics/Optimizersv4/wrapping/itkOptimizerParameterScalesEstimator.wrap -+++ b/Modules/Numerics/Optimizersv4/wrapping/itkOptimizerParameterScalesEstimator.wrap -@@ -1 +1,7 @@ --itk_wrap_simple_class("itk::OptimizerParameterScalesEstimator" POINTER) -+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF) -+itk_wrap_include("itkOptimizerParameterScalesEstimator.h") -+itk_wrap_class("itk::OptimizerParameterScalesEstimatorTemplate" POINTER) -+ foreach(t ${WRAP_ITK_REAL}) -+ itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}") -+ endforeach(t) -+itk_end_wrap_class() - diff --git a/sci-libs/itk/files/0005-make-gdcm-helper-library-static.patch b/sci-libs/itk/files/0005-make-gdcm-helper-library-static.patch deleted file mode 100644 index d760ac7ba..000000000 --- a/sci-libs/itk/files/0005-make-gdcm-helper-library-static.patch +++ /dev/null @@ -1,11 +0,0 @@ -diff --git a/Modules/ThirdParty/GDCM/src/CMakeLists.txt b/Modules/ThirdParty/GDCM/src/CMakeLists.txt -index e98077c..70f4286 100644 ---- a/Modules/ThirdParty/GDCM/src/CMakeLists.txt -+++ b/Modules/ThirdParty/GDCM/src/CMakeLists.txt -@@ -1,5 +1,5 @@ - if(ITK_USE_SYSTEM_GDCM) -- add_library(ITKGDCM ITK-GDCM.cxx) -+ add_library(ITKGDCM STATIC ITK-GDCM.cxx) - target_link_libraries(ITKGDCM gdcmDICT gdcmMSFF) - itk_module_target(ITKGDCM) - return() diff --git a/sci-libs/itk/files/itk-5.2.1-fix-castxml-clang-attr-malloc.patch b/sci-libs/itk/files/itk-5.2.1-fix-castxml-clang-attr-malloc.patch new file mode 100644 index 000000000..05c9d5635 --- /dev/null +++ b/sci-libs/itk/files/itk-5.2.1-fix-castxml-clang-attr-malloc.patch @@ -0,0 +1,25 @@ +From: François-Xavier Carton <fx.carton91@gmail.com> +Date: Thu, 9 Jun 2022 14:56:22 +0200 +Subject: [PATCH] fix attr malloc error with recent glibc/gcc + +Recent GCC has support for __attribute__((__malloc__)) with arguments, but clang +does not. castxml uses clang internally. And recent glibc/gcc uses the attribute +with arguments. Mix all this, and you get: + +error: '__malloc__' attribute takes no arguments + +when compiling itk with python wrapping. + +To fix this, we add a define to castxml flags to remove the extra arguments. + +--- a/Wrapping/Generators/CastXML/CMakeLists.txt 2022-06-09 14:53:15.582352715 +0200 ++++ b/Wrapping/Generators/CastXML/CMakeLists.txt 2022-06-09 14:54:38.182351433 +0200 +@@ -237,7 +237,7 @@ + set(_castxml_cc ${_castxml_cc} "-D_HAS_TR1=0") + endif() + else() +- set(_castxml_cc --castxml-cc-gnu ( "${CMAKE_CXX_COMPILER}" ${_castxml_cc_flags} )) ++ set(_castxml_cc --castxml-cc-gnu ( "${CMAKE_CXX_COMPILER}" ${_castxml_cc_flags} -D__malloc__\(a,b\)=__malloc__ )) + endif() + set(_target) + if(CMAKE_CROSSCOMPILING) diff --git a/sci-libs/itk/files/itk-5.2.1-system-openjpeg.patch b/sci-libs/itk/files/itk-5.2.1-system-openjpeg.patch new file mode 100644 index 000000000..ad717f677 --- /dev/null +++ b/sci-libs/itk/files/itk-5.2.1-system-openjpeg.patch @@ -0,0 +1,558 @@ +--- a/Modules/ThirdParty/OpenJPEG/CMakeLists.txt ++++ b/Modules/ThirdParty/OpenJPEG/CMakeLists.txt +@@ -1,16 +1,32 @@ + project(ITKOpenJPEG) + set(ITKOpenJPEG_THIRD_PARTY 1) + +-set(ITKOpenJPEG_INCLUDE_DIRS +- ${ITKOpenJPEG_BINARY_DIR}/src/openjpeg +- ${ITKOpenJPEG_SOURCE_DIR}/src/openjpeg +- ) +-set(ITKOpenJPEG_LIBRARIES itkopenjpeg) ++option(ITK_USE_SYSTEM_OPENJPEG "Use system-installed openjpeg" ${ITK_USE_SYSTEM_LIBRARIES}) ++mark_as_advanced(ITK_USE_SYSTEM_OPENJPEG) ++ ++if(ITK_USE_SYSTEM_OPENJPEG) ++ find_package(OpenJPEG REQUIRED) ++ set(ITKOpenJPEG_INCLUDE_DIRS ++ ${ITKOpenJPEG_BINARY_DIR}/src ++ ) ++ set(ITKOpenJPEG_SYSTEM_INCLUDE_DIRS ++ ${OPENJPEG_INCLUDE_DIRS} ++ ) ++ set(ITKOpenJPEG_LIBRARIES "${OPENJPEG_LIBRARIES}") ++ set(ITKOpenJPEG_NO_SRC 1) ++else() ++ set(ITKOpenJPEG_INCLUDE_DIRS ++ ${ITKOpenJPEG_BINARY_DIR}/src/openjpeg ++ ${ITKOpenJPEG_SOURCE_DIR}/src/openjpeg ++ ) ++ set(ITKOpenJPEG_LIBRARIES itkopenjpeg) ++endif() ++ ++configure_file(src/itk_openjpeg.h.in src/itk_openjpeg.h) + set(ITK_LIBRARY_PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS FALSE) +- + itk_module_impl() + +-install(FILES ${ITKOpenJPEG_SOURCE_DIR}/src/itk_openjpeg.h ++install(FILES ${ITKOpenJPEG_BINARY_DIR}/src/itk_openjpeg.h + DESTINATION ${ITKOpenJPEG_INSTALL_INCLUDE_DIR} + COMPONENT Development + ) +diff --git a/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h b/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in +rename from Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h +rename to Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in +--- a/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h ++++ b/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in +@@ -25,6 +25,12 @@ + #ifndef itk_openjpeg_h + #define itk_openjpeg_h + +-#include <itkopenjpeg/openjpeg.h> ++/* Use the openjpeg library configured for ITK. */ ++#cmakedefine ITK_USE_SYSTEM_OPENJPEG ++#ifdef ITK_USE_SYSTEM_OPENJPEG ++# include <openjpeg.h> ++#else ++# include <itkopenjpeg/openjpeg.h> ++#endif + + #endif +--- a/Modules/IO/JPEG2000/src/itkJPEG2000ImageIO.cxx ++++ b/Modules/IO/JPEG2000/src/itkJPEG2000ImageIO.cxx +@@ -27,8 +27,6 @@ + extern "C" + { + #include "openjpeg.h" +-#include "j2k.h" +-#include "jp2.h" + } + + +@@ -139,11 +137,11 @@ + { + itkDebugMacro(<< "ReadImageInformation()"); + +- FILE * l_file = fopen(this->m_FileName.c_str(), "rb"); +- +- /* decompression parameters */ ++ /* set decoding parameters to default values */ ++ opj_set_default_decoder_parameters(&(this->m_Internal->m_DecompressionParameters)); + +- if (!l_file) ++ opj_stream_t * cio = opj_stream_create_default_file_stream(this->m_FileName.c_str(), true); ++ if (!cio) + { + itkExceptionMacro("JPEG2000ImageIO failed to open file for reading: " << this->GetFileName() << std::endl + << "Reason: " +@@ -151,10 +149,5 @@ + } + +- /* set decoding parameters to default values */ +- opj_set_default_decoder_parameters(&(this->m_Internal->m_DecompressionParameters)); +- +- opj_stream_t * cio = opj_stream_create_default_file_stream(l_file, true); +- + this->m_Internal->m_Dinfo = nullptr; /* handle to a decompressor */ + + opj_image_t * l_image = nullptr; +@@ -188,9 +181,8 @@ + + /* get a decoder handle */ +- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_J2K); ++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_J2K); + if (!this->m_Internal->m_Dinfo) + { + opj_stream_destroy(cio); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl +@@ -202,10 +194,9 @@ + { + /* JPEG 2000 compressed image data */ + /* get a decoder handle */ +- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JP2); ++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JP2); + if (!this->m_Internal->m_Dinfo) + { + opj_stream_destroy(cio); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl +@@ -217,10 +208,9 @@ + { + /* JPEG 2000, JPIP */ + /* get a decoder handle */ +- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JPT); ++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JPT); + if (!this->m_Internal->m_Dinfo) + { + opj_stream_destroy(cio); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl +@@ -230,7 +220,6 @@ + } + default: + opj_stream_destroy(cio); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl + << "Reason: " +@@ -248,26 +237,8 @@ + } + +- // Image parameters - first tile +- OPJ_INT32 l_tile_x0; +- OPJ_INT32 l_tile_y0; +- +- // Image parameters - tile width, height and number of tiles +- OPJ_UINT32 l_tile_width; +- OPJ_UINT32 l_tile_height; +- OPJ_UINT32 l_nb_tiles_x; +- OPJ_UINT32 l_nb_tiles_y; +- + itkDebugMacro(<< "Trying to read header now..."); + +- bResult = opj_read_header(this->m_Internal->m_Dinfo, +- &l_image, +- &l_tile_x0, +- &l_tile_y0, +- &l_tile_width, +- &l_tile_height, +- &l_nb_tiles_x, +- &l_nb_tiles_y, +- cio); ++ bResult = opj_read_header(cio, this->m_Internal->m_Dinfo, &l_image); + + if (!bResult) + { +@@ -284,13 +255,21 @@ + } + +- this->m_Internal->m_TileStartX = l_tile_x0; +- this->m_Internal->m_TileStartY = l_tile_y0; ++ opj_codestream_info_v2_t* cp = opj_get_cstr_info(this->m_Internal->m_Dinfo); ++ if (!cp) ++ { ++ opj_stream_destroy(cio); ++ opj_image_destroy(l_image); ++ itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl ++ << "Reason: Error while reading image header"); ++ } ++ this->m_Internal->m_TileStartX = cp->tx0; ++ this->m_Internal->m_TileStartY = cp->ty0; + +- this->m_Internal->m_TileWidth = l_tile_width; +- this->m_Internal->m_TileHeight = l_tile_height; ++ this->m_Internal->m_TileWidth = cp->tdx; ++ this->m_Internal->m_TileHeight = cp->tdy; + +- this->m_Internal->m_NumberOfTilesInX = l_nb_tiles_x; +- this->m_Internal->m_NumberOfTilesInY = l_nb_tiles_y; ++ this->m_Internal->m_NumberOfTilesInX = cp->tw; ++ this->m_Internal->m_NumberOfTilesInY = cp->th; + + + itkDebugMacro(<< "Number of Components = " << l_image->numcomps); +@@ -307,6 +286,7 @@ + else + { + opj_stream_destroy(cio); ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl + << "Reason: " + << "Unknown precision in file: " +@@ -320,6 +300,6 @@ + break; + case 3: +- if (l_image->color_space != CLRSPC_SRGB) ++ if (l_image->color_space != OPJ_CLRSPC_SRGB) + { + itkWarningMacro(<< "file does not specify color space, assuming sRGB"); + } +@@ -349,7 +329,6 @@ + + /* close the byte stream */ + opj_stream_destroy(cio); +- fclose(l_file); + + if (this->m_Internal->m_Dinfo) + { +@@ -368,16 +347,7 @@ + { + itkDebugMacro(<< "JPEG2000ImageIO::Read() Begin"); + +- FILE * l_file = fopen(this->m_FileName.c_str(), "rb"); +- +- if (!l_file) +- { +- itkExceptionMacro("JPEG2000ImageIO failed to open file for reading: " << this->GetFileName() << std::endl +- << "Reason: " +- << itksys::SystemTools::GetLastSystemError()); +- } +- +- opj_stream_t * l_stream = opj_stream_create_default_file_stream(l_file, true); ++ opj_stream_t * l_stream = opj_stream_create_default_file_stream(this->m_FileName.c_str(), true); + if (!l_stream) + { + itkExceptionMacro("JPEG2000ImageIO failed to read file: " +@@ -397,9 +367,10 @@ + { + /* JPEG-2000 codestream */ + /* get a decoder handle */ +- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_J2K); ++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_J2K); + if (!this->m_Internal->m_Dinfo) + { ++ opj_stream_destroy(l_stream); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl + << "Reason: opj_create_decompress(CODEC_J2K) returns nullptr"); +@@ -410,9 +381,10 @@ + { + /* JPEG 2000 compressed image data */ + /* get a decoder handle */ +- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JP2); ++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JP2); + if (!this->m_Internal->m_Dinfo) + { ++ opj_stream_destroy(l_stream); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl + << "Reason: opj_create_decompress(CODEC_JP2) returns nullptr"); +@@ -423,9 +395,10 @@ + { + /* JPEG 2000, JPIP */ + /* get a decoder handle */ +- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JPT); ++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JPT); + if (!this->m_Internal->m_Dinfo) + { ++ opj_stream_destroy(l_stream); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl + << "Reason: opj_create_decompress(CODEC_JPT) returns nullptr"); +@@ -433,7 +406,7 @@ + break; + } + default: +- fclose(l_file); ++ opj_stream_destroy(l_stream); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl + << "Reason: " +@@ -445,32 +418,17 @@ + if (!opj_setup_decoder(this->m_Internal->m_Dinfo, &(this->m_Internal->m_DecompressionParameters))) + { ++ opj_stream_destroy(l_stream); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl + << "Reason: opj_setup_decoder returns false"); + } + +- OPJ_INT32 l_tile_x0, l_tile_y0; +- +- OPJ_UINT32 l_tile_width; +- OPJ_UINT32 l_tile_height; +- OPJ_UINT32 l_nb_tiles_x; +- OPJ_UINT32 l_nb_tiles_y; +- +- bool bResult = opj_read_header(this->m_Internal->m_Dinfo, +- &l_image, +- &l_tile_x0, +- &l_tile_y0, +- &l_tile_width, +- &l_tile_height, +- &l_nb_tiles_x, +- &l_nb_tiles_y, +- l_stream); ++ bool bResult = opj_read_header(l_stream, this->m_Internal->m_Dinfo, &l_image); + + if (!bResult) + { + opj_destroy_codec(this->m_Internal->m_Dinfo); + this->m_Internal->m_Dinfo = nullptr; + opj_stream_destroy(l_stream); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl + << "Reason: opj_read_header returns false"); + } +@@ -499,7 +457,7 @@ + itkDebugMacro(<< "p_end_x = " << p_end_x); + itkDebugMacro(<< "p_end_y = " << p_end_y); + +- bResult = opj_set_decode_area(this->m_Internal->m_Dinfo, p_start_x, p_start_y, p_end_x, p_end_y); ++ bResult = opj_set_decode_area(this->m_Internal->m_Dinfo, l_image, p_start_x, p_start_y, p_end_x, p_end_y); + + itkDebugMacro(<< "opj_set_decode_area() after"); + +@@ -509,6 +467,5 @@ + this->m_Internal->m_Dinfo = nullptr; + opj_stream_destroy(l_stream); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl + << "Reason: opj_set_decode_area returns false"); + } +@@ -525,13 +482,14 @@ + + OPJ_UINT32 l_max_data_size = 1000; + +- bool l_go_on = true; ++ OPJ_BOOL l_go_on = true; + + auto * l_data = (OPJ_BYTE *)malloc(1000); + + while (l_go_on) + { + bool tileHeaderRead = opj_read_tile_header(this->m_Internal->m_Dinfo, ++ l_stream, + &l_tile_index, + &l_data_size, + &l_current_tile_x0, +@@ -540,13 +498,11 @@ + &l_current_tile_y1, + &l_nb_comps, +- &l_go_on, +- l_stream); ++ &l_go_on); + + if (!tileHeaderRead) + { + free(l_data); + opj_stream_destroy(l_stream); +- fclose(l_file); + opj_destroy_codec(this->m_Internal->m_Dinfo); + opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl +@@ -571,7 +527,6 @@ + if (!l_data) + { + opj_stream_destroy(l_stream); +- fclose(l_file); + opj_destroy_codec(this->m_Internal->m_Dinfo); + opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl +@@ -590,7 +545,6 @@ + { + free(l_data); + opj_stream_destroy(l_stream); +- fclose(l_file); + opj_destroy_codec(this->m_Internal->m_Dinfo); + opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl +@@ -654,7 +608,6 @@ + { + free(l_data); + opj_stream_destroy(l_stream); +- fclose(l_file); + opj_destroy_codec(this->m_Internal->m_Dinfo); + opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl +@@ -667,13 +620,11 @@ + this->m_Internal->m_Dinfo = nullptr; + opj_stream_destroy(l_stream); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl + << "Reason: error whle reading image"); + } + + /* close the byte stream */ + opj_stream_destroy(l_stream); +- fclose(l_file); + + if (this->m_Internal->m_Dinfo) + { +@@ -775,6 +726,6 @@ + } + +- for (int i = 0; i < parameters.numpocs; i++) ++ for (OPJ_UINT32 i = 0; i < parameters.numpocs; i++) + { + if (parameters.POC[i].prg == -1) + { +@@ -840,13 +791,13 @@ + + parameters.numresolution = numberOfResolutions; + +- OPJ_COLOR_SPACE color_space = CLRSPC_GRAY; ++ OPJ_COLOR_SPACE color_space = OPJ_CLRSPC_GRAY; + opj_image_cmptparm_t cmptparms[3]; + + if (this->GetNumberOfComponents() == 3) + { + +- color_space = (this->GetPixelType() == IOPixelEnum::RGB) ? CLRSPC_SRGB : CLRSPC_UNSPECIFIED; ++ color_space = (this->GetPixelType() == IOPixelEnum::RGB) ? OPJ_CLRSPC_SRGB : OPJ_CLRSPC_UNSPECIFIED; + + /* initialize image components */ + memset(&cmptparms[0], 0, 3 * sizeof(opj_image_cmptparm_t)); +@@ -864,7 +815,7 @@ + + if (this->GetNumberOfComponents() == 1) + { +- color_space = CLRSPC_GRAY; ++ color_space = OPJ_CLRSPC_GRAY; + + /* initialize image components */ + memset(&cmptparms[0], 0, sizeof(opj_image_cmptparm_t)); +@@ -941,8 +892,9 @@ + if (extension == ".j2k") + { +- cinfo = opj_create_compress(CODEC_J2K); ++ cinfo = opj_create_compress(OPJ_CODEC_J2K); + if (!cinfo) + { ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " + << this->GetFileName() << std::endl + << "Reason: opj_create_compress(CODEC_J2K) returns nullptr"); +@@ -950,9 +902,10 @@ + } + else if (extension == ".jp2") + { +- cinfo = opj_create_compress(CODEC_JP2); ++ cinfo = opj_create_compress(OPJ_CODEC_JP2); + if (!cinfo) + { ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " + << this->GetFileName() << std::endl + << "Reason: opj_create_compress(CODEC_JP2) returns nullptr"); +@@ -960,9 +913,10 @@ + } + else if (extension == ".jpt") + { +- cinfo = opj_create_compress(CODEC_JPT); ++ cinfo = opj_create_compress(OPJ_CODEC_JPT); + if (!cinfo) + { ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " + << this->GetFileName() << std::endl + << "Reason: opj_create_compress(CODEC_JPT) returns nullptr"); +@@ -970,6 +924,7 @@ + } + else + { ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl + << "Reason: unknown encode format: " << extension); + } +@@ -985,23 +940,19 @@ + + if (!opj_setup_encoder(cinfo, ¶meters, l_image)) + { ++ opj_destroy_codec(cinfo); ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl + << "Reason: opj_setup_encoder returns false"); + } + +- FILE * l_file = fopen(parameters.outfile, "wb"); +- if (!l_file) +- { +- itkExceptionMacro("JPEG2000ImageIO failed to open file for writing: " << this->GetFileName() << std::endl +- << "Reason: " +- << itksys::SystemTools::GetLastSystemError()); +- } +- + /* open a byte stream for writing */ + /* allocate memory for all tiles */ +- opj_stream_t * cio = opj_stream_create_default_file_stream(l_file, false); ++ opj_stream_t * cio = opj_stream_create_default_file_stream(parameters.outfile, false); + if (!cio) + { ++ opj_destroy_codec(cinfo); ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " + << this->GetFileName() << std::endl + << "Reason: " +@@ -1017,7 +968,8 @@ + if (!bSuccess) + { + opj_stream_destroy(cio); +- fclose(l_file); ++ opj_destroy_codec(cinfo); ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl + << "Reason: opj_start_compress returns false"); + } +@@ -1026,7 +978,8 @@ + if (!bSuccess) + { + opj_stream_destroy(cio); +- fclose(l_file); ++ opj_destroy_codec(cinfo); ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl + << "Reason: opj_encode returns false"); + } +@@ -1035,14 +988,14 @@ + if (!bSuccess) + { + opj_stream_destroy(cio); +- fclose(l_file); ++ opj_destroy_codec(cinfo); ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl + << "Reason: opj_end_compress returns false"); + } + + /* close and free the byte stream */ + opj_stream_destroy(cio); +- fclose(l_file); + + /* free remaining compression structures */ + opj_destroy_codec(cinfo); +--- a/Modules/Nonunit/Review/src/CMakeLists.txt ++++ b/Modules/Nonunit/Review/src/CMakeLists.txt +@@ -5,7 +5,7 @@ + + add_library(ITKReview ${ITKReview_SRC}) + itk_module_link_dependencies() +-target_link_libraries(ITKReview LINK_PUBLIC ${ITKTestKernel_LIBRARIES} ${ITKIOLSM_LIBRARIES} itkopenjpeg) ++target_link_libraries(ITKReview LINK_PUBLIC ${ITKTestKernel_LIBRARIES} ${ITKIOLSM_LIBRARIES} ${ITKOpenJPEG_LIBRARIES}) + itk_module_target(ITKReview) + + diff --git a/sci-libs/itk/files/itk-5.2.1-system-tiff-has-64.patch b/sci-libs/itk/files/itk-5.2.1-system-tiff-has-64.patch new file mode 100644 index 000000000..25c44db2c --- /dev/null +++ b/sci-libs/itk/files/itk-5.2.1-system-tiff-has-64.patch @@ -0,0 +1,18 @@ +From: François-Xavier Carton <fx.carton91@gmail.com> +Date: Wed, 8 Jun 2022 19:36:48 +0200 +Subject: [PATCH] system libtiff has INT64 + +Enabling this, otherwise using system libtiff leads to errors. In particular +tests fail because there is some IFD8 data but the itkTIFFDataSize function +returns 0 instead of 8, resulting in invalid mem access. + +--- a/Modules/ThirdParty/TIFF/src/itk_tiff.h.in.orig 2022-06-08 19:34:04.412431969 +0200 ++++ b/Modules/ThirdParty/TIFF/src/itk_tiff.h.in 2022-06-08 19:34:26.240431631 +0200 +@@ -34,6 +34,7 @@ + #cmakedefine ITK_TIFF_HAS_TIFFFieldReadCount + #cmakedefine ITK_TIFF_HAS_TIFFField + #ifdef ITK_USE_SYSTEM_TIFF ++# define TIFF_INT64_T int64_t + # include <tiffio.h> + #else + # include "itktiff/tiffio.h" diff --git a/sci-libs/itk/files/itk-5.2.1-upstream-fixes.patch b/sci-libs/itk/files/itk-5.2.1-upstream-fixes.patch new file mode 100644 index 000000000..2af8c4998 --- /dev/null +++ b/sci-libs/itk/files/itk-5.2.1-upstream-fixes.patch @@ -0,0 +1,309 @@ +https://github.com/InsightSoftwareConsortium/ITK/commit/2a7f5ed199926999b67f61a97c2c9a2595a11558.patch +https://github.com/InsightSoftwareConsortium/ITK/commit/0c31aa688e82a34e5430873bc6176740fd09ad75.patch +https://github.com/InsightSoftwareConsortium/ITK/commit/28325d921a9b8793e6aaefd612f53989f951d19c.patch +https://github.com/InsightSoftwareConsortium/ITK/commit/aafd1f9631d0fad60e1b6f53e049e95a50c48bd1.patch + +From 2a7f5ed199926999b67f61a97c2c9a2595a11558 Mon Sep 17 00:00:00 2001 +From: Niels Dekker <N.Dekker@lumc.nl> +Date: Thu, 24 Jun 2021 18:00:01 +0200 +Subject: [PATCH] COMP: Add missing `#include <iostream>` to Deprecated module + test + +Fixed a Visual C++ 2019 error, saying: + +> Deprecated\test\itkSimpleFastMutexLockTest.cxx(48,12): error C2039: 'cout': is not a member of 'std' +--- + .../Deprecated/test/itkSimpleFastMutexLockTest.cxx | 2 ++ + 1 file changed, 2 insertions(+) + +diff --git a/Modules/Compatibility/Deprecated/test/itkSimpleFastMutexLockTest.cxx b/Modules/Compatibility/Deprecated/test/itkSimpleFastMutexLockTest.cxx +index 11ad0c52700..60aa1c065b4 100644 +--- a/Modules/Compatibility/Deprecated/test/itkSimpleFastMutexLockTest.cxx ++++ b/Modules/Compatibility/Deprecated/test/itkSimpleFastMutexLockTest.cxx +@@ -19,6 +19,8 @@ + + #include "itkSimpleFastMutexLock.h" + ++#include <iostream> // For cout. ++ + + int + itkSimpleFastMutexLockTest(int, char *[]) +From 0c31aa688e82a34e5430873bc6176740fd09ad75 Mon Sep 17 00:00:00 2001 +From: Pablo Hernandez-Cerdan <pablo.hernandez.cerdan@outlook.com> +Date: Tue, 20 Apr 2021 17:21:21 +0200 +Subject: [PATCH] COMP: CastXML, ITKVtkGlue, include only when property exists + +Some targets (VTK libraries) didn't have the property INTERFACE_INCLUDE_DIRECTORIES + +```bash +CMake Error in Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt: + Found relative path while evaluating include directories of + "ITKVtkGluePython": + + "_vtk_lib_include_dirs-NOTFOUND" +``` + +Triggered when compiling Slicer with `Slicer_BUILD_ITKPython:BOOL=ON` +aka `ITK_WRAP_PYTHON:BOOL=ON`. + +Full error log with extra printing: + +```bash + +CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:3 (message): + ITKVtkGlue_VTK_LIBRARIES: + VTK::IOImage;VTK::ImagingSources;VTK::WrappingPythonCore;VTK::CommonCore;VTK::CommonDataModel;VTK::kwiml;VTK::CommonExecutionModel;VTK::RenderingOpenGL2;VTK::RenderingFreeType;VTK::InteractionStyle;VTK::InteractionWidgets + +CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message): + _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND + +CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message): + _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND + +CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message): + _vtk_lib_include_dirs: + build/VTK-build/Wrapping/PythonCore;build/VTK/Wrapping/PythonCore + +CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message): + _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND + +CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message): + _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND + +CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message): + _vtk_lib_include_dirs: + build/VTK-build/Utilities/KWIML;build/VTK/Utilities/KWIML + +CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message): + _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND + +CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message): + _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND + +CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message): + _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND + +CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message): + _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND + +CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message): + _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND + +-- ITKVtkGlue: Creating module. +-- ITKVtkGlue: Creating itkImageToVTKImageFilter submodule. +-- ITKVtkGlue: Creating itkVTKImageToImageFilter submodule. +-- ITKVtkGlue: Creating itkViewImage submodule. +-- MGHIO: Creating module. +-- MGHIO: Creating itkMGHImageIO submodule. +-- MorphologicalContourInterpolation: Creating module. +-- MorphologicalContourInterpolation: Creating itkMorphologicalContourInterpolator submodule. +-- ITKPyUtils: Creating module. +-- ITKPyUtils: Creating itkPyCommand submodule. +-- ITKPyUtils: Creating itkPyImageFilter submodule. +-- Configuring done +CMake Error: The following variables are used in this project, but they are set to NOTFOUND. +Please set them or make sure they are set and tested correctly in the CMake files: +_vtk_lib_include_dirs + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + +CMake Error in Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt: + Found relative path while evaluating include directories of + "ITKVtkGluePython": + + "_vtk_lib_include_dirs-NOTFOUND" + +``` +--- + Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt | 4 +++- + 1 file changed, 3 insertions(+), 1 deletion(-) + +diff --git a/Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt b/Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt +index 3f3322957e1..2fd6a5af8f6 100644 +--- a/Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt ++++ b/Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt +@@ -2,7 +2,9 @@ + if(NOT VTK_RENDERING_BACKEND STREQUAL "None") + foreach(_vtk_lib IN LISTS ITKVtkGlue_VTK_LIBRARIES) + get_target_property(_vtk_lib_include_dirs ${_vtk_lib} INTERFACE_INCLUDE_DIRECTORIES) +- include_directories(${_vtk_lib_include_dirs}) ++ if(_vtk_lib_include_dirs) ++ include_directories(${_vtk_lib_include_dirs}) ++ endif() + endforeach() + endif() + +From 28325d921a9b8793e6aaefd612f53989f951d19c Mon Sep 17 00:00:00 2001 +From: Butui Hu <hot123tea123@gmail.com> +Date: Mon, 1 Aug 2022 14:26:39 +0800 +Subject: [PATCH] COMP: use sysconfig.get_path as PEP 632 deprecate distutils + module + +--- + Wrapping/Generators/Python/CMakeLists.txt | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/Wrapping/Generators/Python/CMakeLists.txt b/Wrapping/Generators/Python/CMakeLists.txt +index fca3d999b87..3b7a1d37334 100644 +--- a/Wrapping/Generators/Python/CMakeLists.txt ++++ b/Wrapping/Generators/Python/CMakeLists.txt +@@ -36,7 +36,7 @@ file(MAKE_DIRECTORY ${WRAPPER_MASTER_INDEX_OUTPUT_DIR}/python) + ############################################################################### + # Configure Python wrapping installation + if(Python3_EXECUTABLE AND NOT PY_SITE_PACKAGES_PATH) +- set(python_check "try:\n import distutils.sysconfig\n print(distutils.sysconfig.get_python_lib(plat_specific=1, prefix=''))\nexcept:\n pass") ++ set(python_check "try:\n import sysconfig\n print(sysconfig.get_path('platlib'))\nexcept:\n pass") + file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/detect_site_package_path.py ${python_check}) + execute_process(COMMAND "${Python3_EXECUTABLE}" "${CMAKE_CURRENT_BINARY_DIR}/detect_site_package_path.py" + OUTPUT_VARIABLE py_spp +From aafd1f9631d0fad60e1b6f53e049e95a50c48bd1 Mon Sep 17 00:00:00 2001 +From: Hans Johnson <hans-johnson@uiowa.edu> +Date: Wed, 15 Dec 2021 08:10:58 -0600 +Subject: [PATCH] COMP: Remove inclusion of .hxx files as headers + +The ability to include either .h or .hxx files as +header files required recursively reading the +.h files twice. The added complexity is +unnecessary, costly, and can confuse static +analysis tools that monitor header guardes (due +to reaching the maximum depth of recursion +limits for nested #ifdefs in checking). + +Co-authored-by: Simon Rit <simon.rit@creatis.insa-lyon.fr> +--- + CMake/ITKModuleHeaderTest.cmake | 3 +-- + Utilities/Maintenance/BuildHeaderTest.py | 4 ---- + 2 files changed, 1 insertion(+), 6 deletions(-) + +diff --git a/CMake/ITKModuleHeaderTest.cmake b/CMake/ITKModuleHeaderTest.cmake +index eb809d7e93d..82ad192a6f8 100644 +--- a/CMake/ITKModuleHeaderTest.cmake ++++ b/CMake/ITKModuleHeaderTest.cmake +@@ -36,8 +36,7 @@ macro( itk_module_headertest _name ) + # effected. + set( _include ${${_name}_SOURCE_DIR}/include ) + file( GLOB _h_files ${_include}/*.h ) +- file( GLOB _hxx_files ${_include}/*.hxx ) +- set( _header_files ${_h_files} ${_hxx_files} ) ++ set( _header_files ${_h_files} ) + list( LENGTH _h_files _num_headers ) + set( _outputs ${${_name}_BINARY_DIR}/test/${_name}HeaderTest1.cxx ) + set( _test_num 1 ) +diff --git a/Utilities/Maintenance/BuildHeaderTest.py b/Utilities/Maintenance/BuildHeaderTest.py +index 26a4b6ccb3f..f8ed9f7901e 100755 +--- a/Utilities/Maintenance/BuildHeaderTest.py ++++ b/Utilities/Maintenance/BuildHeaderTest.py +@@ -130,15 +130,11 @@ def main(): + else: + max_idx = added_header_idx + maximum_number_of_headers + for i in range(added_header_idx, max_idx): +- # Use the .hxx if possible. +- hxx_file = h_files[i][:-1] + "hxx" + # Files that include VTK headers need to link to VTK. + if h_files[i] in BANNED_HEADERS or h_files[i].lower().find("vtk") != -1: + to_include = ( + '// #include "' + h_files[i] + '" // Banned in BuildHeaderTest.py\n' + ) +- elif os.path.exists(os.path.join(module_source_path, "include", hxx_file)): +- to_include = '#include "' + hxx_file + '"\n' + else: + to_include = '#include "' + h_files[i] + '"\n' + diff --git a/sci-libs/itk/files/itk-5.3.0-system-openjpeg.patch b/sci-libs/itk/files/itk-5.3.0-system-openjpeg.patch new file mode 100644 index 000000000..27f139553 --- /dev/null +++ b/sci-libs/itk/files/itk-5.3.0-system-openjpeg.patch @@ -0,0 +1,550 @@ +--- a/Modules/ThirdParty/OpenJPEG/CMakeLists.txt ++++ b/Modules/ThirdParty/OpenJPEG/CMakeLists.txt +@@ -1,16 +1,32 @@ + project(ITKOpenJPEG) + set(ITKOpenJPEG_THIRD_PARTY 1) + +-set(ITKOpenJPEG_INCLUDE_DIRS +- ${ITKOpenJPEG_BINARY_DIR}/src/openjpeg +- ${ITKOpenJPEG_SOURCE_DIR}/src/openjpeg +- ) +-set(ITKOpenJPEG_LIBRARIES itkopenjpeg) ++option(ITK_USE_SYSTEM_OPENJPEG "Use system-installed openjpeg" ${ITK_USE_SYSTEM_LIBRARIES}) ++mark_as_advanced(ITK_USE_SYSTEM_OPENJPEG) ++ ++if(ITK_USE_SYSTEM_OPENJPEG) ++ find_package(OpenJPEG REQUIRED) ++ set(ITKOpenJPEG_INCLUDE_DIRS ++ ${ITKOpenJPEG_BINARY_DIR}/src ++ ) ++ set(ITKOpenJPEG_SYSTEM_INCLUDE_DIRS ++ ${OPENJPEG_INCLUDE_DIRS} ++ ) ++ set(ITKOpenJPEG_LIBRARIES "${OPENJPEG_LIBRARIES}") ++ set(ITKOpenJPEG_NO_SRC 1) ++else() ++ set(ITKOpenJPEG_INCLUDE_DIRS ++ ${ITKOpenJPEG_BINARY_DIR}/src/openjpeg ++ ${ITKOpenJPEG_SOURCE_DIR}/src/openjpeg ++ ) ++ set(ITKOpenJPEG_LIBRARIES itkopenjpeg) ++endif() ++ ++configure_file(src/itk_openjpeg.h.in src/itk_openjpeg.h) + set(ITK_LIBRARY_PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS FALSE) +- + itk_module_impl() + +-install(FILES ${ITKOpenJPEG_SOURCE_DIR}/src/itk_openjpeg.h ++install(FILES ${ITKOpenJPEG_BINARY_DIR}/src/itk_openjpeg.h + DESTINATION ${ITKOpenJPEG_INSTALL_INCLUDE_DIR} + COMPONENT Development + ) +diff --git a/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h b/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in +rename from Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h +rename to Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in +--- a/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h ++++ b/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in +@@ -25,6 +25,12 @@ + #ifndef itk_openjpeg_h + #define itk_openjpeg_h + +-#include <itkopenjpeg/openjpeg.h> ++/* Use the openjpeg library configured for ITK. */ ++#cmakedefine ITK_USE_SYSTEM_OPENJPEG ++#ifdef ITK_USE_SYSTEM_OPENJPEG ++# include <openjpeg.h> ++#else ++# include <itkopenjpeg/openjpeg.h> ++#endif + + #endif +--- a/Modules/IO/JPEG2000/src/itkJPEG2000ImageIO.cxx ++++ b/Modules/IO/JPEG2000/src/itkJPEG2000ImageIO.cxx +@@ -27,8 +27,6 @@ + extern "C" + { + #include "openjpeg.h" +-#include "j2k.h" +-#include "jp2.h" + } + + +@@ -139,11 +137,11 @@ + { + itkDebugMacro(<< "ReadImageInformation()"); + +- FILE * l_file = fopen(this->m_FileName.c_str(), "rb"); +- +- /* decompression parameters */ ++ /* set decoding parameters to default values */ ++ opj_set_default_decoder_parameters(&(this->m_Internal->m_DecompressionParameters)); + +- if (!l_file) ++ opj_stream_t * cio = opj_stream_create_default_file_stream(this->m_FileName.c_str(), true); ++ if (!cio) + { + itkExceptionMacro("JPEG2000ImageIO failed to open file for reading: " << this->GetFileName() << std::endl + << "Reason: " +@@ -151,10 +149,5 @@ + } + +- /* set decoding parameters to default values */ +- opj_set_default_decoder_parameters(&(this->m_Internal->m_DecompressionParameters)); +- +- opj_stream_t * cio = opj_stream_create_default_file_stream(l_file, true); +- + this->m_Internal->m_Dinfo = nullptr; /* handle to a decompressor */ + + opj_image_t * l_image = nullptr; +@@ -188,9 +181,8 @@ + + /* get a decoder handle */ +- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_J2K); ++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_J2K); + if (!this->m_Internal->m_Dinfo) + { + opj_stream_destroy(cio); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl +@@ -202,10 +194,9 @@ + { + /* JPEG 2000 compressed image data */ + /* get a decoder handle */ +- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JP2); ++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JP2); + if (!this->m_Internal->m_Dinfo) + { + opj_stream_destroy(cio); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl +@@ -217,10 +208,9 @@ + { + /* JPEG 2000, JPIP */ + /* get a decoder handle */ +- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JPT); ++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JPT); + if (!this->m_Internal->m_Dinfo) + { + opj_stream_destroy(cio); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl +@@ -230,7 +220,6 @@ + } + default: + opj_stream_destroy(cio); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl + << "Reason: " +@@ -248,26 +237,8 @@ + } + +- // Image parameters - first tile +- OPJ_INT32 l_tile_x0; +- OPJ_INT32 l_tile_y0; +- +- // Image parameters - tile width, height and number of tiles +- OPJ_UINT32 l_tile_width; +- OPJ_UINT32 l_tile_height; +- OPJ_UINT32 l_nb_tiles_x; +- OPJ_UINT32 l_nb_tiles_y; +- + itkDebugMacro(<< "Trying to read header now..."); + +- bResult = opj_read_header(this->m_Internal->m_Dinfo, +- &l_image, +- &l_tile_x0, +- &l_tile_y0, +- &l_tile_width, +- &l_tile_height, +- &l_nb_tiles_x, +- &l_nb_tiles_y, +- cio); ++ bResult = opj_read_header(cio, this->m_Internal->m_Dinfo, &l_image); + + if (!bResult) + { +@@ -284,13 +255,21 @@ + } + +- this->m_Internal->m_TileStartX = l_tile_x0; +- this->m_Internal->m_TileStartY = l_tile_y0; ++ opj_codestream_info_v2_t* cp = opj_get_cstr_info(this->m_Internal->m_Dinfo); ++ if (!cp) ++ { ++ opj_stream_destroy(cio); ++ opj_image_destroy(l_image); ++ itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl ++ << "Reason: Error while reading image header"); ++ } ++ this->m_Internal->m_TileStartX = cp->tx0; ++ this->m_Internal->m_TileStartY = cp->ty0; + +- this->m_Internal->m_TileWidth = l_tile_width; +- this->m_Internal->m_TileHeight = l_tile_height; ++ this->m_Internal->m_TileWidth = cp->tdx; ++ this->m_Internal->m_TileHeight = cp->tdy; + +- this->m_Internal->m_NumberOfTilesInX = l_nb_tiles_x; +- this->m_Internal->m_NumberOfTilesInY = l_nb_tiles_y; ++ this->m_Internal->m_NumberOfTilesInX = cp->tw; ++ this->m_Internal->m_NumberOfTilesInY = cp->th; + + + itkDebugMacro(<< "Number of Components = " << l_image->numcomps); +@@ -307,6 +286,7 @@ + else + { + opj_stream_destroy(cio); ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl + << "Reason: " + << "Unknown precision in file: " +@@ -320,6 +300,6 @@ + break; + case 3: +- if (l_image->color_space != CLRSPC_SRGB) ++ if (l_image->color_space != OPJ_CLRSPC_SRGB) + { + itkWarningMacro(<< "file does not specify color space, assuming sRGB"); + } +@@ -349,7 +329,6 @@ + + /* close the byte stream */ + opj_stream_destroy(cio); +- fclose(l_file); + + if (this->m_Internal->m_Dinfo) + { +@@ -368,16 +347,7 @@ + { + itkDebugMacro(<< "JPEG2000ImageIO::Read() Begin"); + +- FILE * l_file = fopen(this->m_FileName.c_str(), "rb"); +- +- if (!l_file) +- { +- itkExceptionMacro("JPEG2000ImageIO failed to open file for reading: " << this->GetFileName() << std::endl +- << "Reason: " +- << itksys::SystemTools::GetLastSystemError()); +- } +- +- opj_stream_t * l_stream = opj_stream_create_default_file_stream(l_file, true); ++ opj_stream_t * l_stream = opj_stream_create_default_file_stream(this->m_FileName.c_str(), true); + if (!l_stream) + { + itkExceptionMacro("JPEG2000ImageIO failed to read file: " +@@ -397,9 +367,10 @@ + { + /* JPEG-2000 codestream */ + /* get a decoder handle */ +- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_J2K); ++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_J2K); + if (!this->m_Internal->m_Dinfo) + { ++ opj_stream_destroy(l_stream); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl + << "Reason: opj_create_decompress(CODEC_J2K) returns nullptr"); +@@ -410,9 +381,10 @@ + { + /* JPEG 2000 compressed image data */ + /* get a decoder handle */ +- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JP2); ++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JP2); + if (!this->m_Internal->m_Dinfo) + { ++ opj_stream_destroy(l_stream); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl + << "Reason: opj_create_decompress(CODEC_JP2) returns nullptr"); +@@ -423,9 +395,10 @@ + { + /* JPEG 2000, JPIP */ + /* get a decoder handle */ +- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JPT); ++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JPT); + if (!this->m_Internal->m_Dinfo) + { ++ opj_stream_destroy(l_stream); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl + << "Reason: opj_create_decompress(CODEC_JPT) returns nullptr"); +@@ -433,7 +406,7 @@ + break; + } + default: +- fclose(l_file); ++ opj_stream_destroy(l_stream); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl + << "Reason: " +@@ -445,32 +418,17 @@ + if (!opj_setup_decoder(this->m_Internal->m_Dinfo, &(this->m_Internal->m_DecompressionParameters))) + { ++ opj_stream_destroy(l_stream); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl + << "Reason: opj_setup_decoder returns false"); + } + +- OPJ_INT32 l_tile_x0, l_tile_y0; +- +- OPJ_UINT32 l_tile_width; +- OPJ_UINT32 l_tile_height; +- OPJ_UINT32 l_nb_tiles_x; +- OPJ_UINT32 l_nb_tiles_y; +- +- bool bResult = opj_read_header(this->m_Internal->m_Dinfo, +- &l_image, +- &l_tile_x0, +- &l_tile_y0, +- &l_tile_width, +- &l_tile_height, +- &l_nb_tiles_x, +- &l_nb_tiles_y, +- l_stream); ++ bool bResult = opj_read_header(l_stream, this->m_Internal->m_Dinfo, &l_image); + + if (!bResult) + { + opj_destroy_codec(this->m_Internal->m_Dinfo); + this->m_Internal->m_Dinfo = nullptr; + opj_stream_destroy(l_stream); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl + << "Reason: opj_read_header returns false"); + } +@@ -499,7 +457,7 @@ + itkDebugMacro(<< "p_end_x = " << p_end_x); + itkDebugMacro(<< "p_end_y = " << p_end_y); + +- bResult = opj_set_decode_area(this->m_Internal->m_Dinfo, p_start_x, p_start_y, p_end_x, p_end_y); ++ bResult = opj_set_decode_area(this->m_Internal->m_Dinfo, l_image, p_start_x, p_start_y, p_end_x, p_end_y); + + itkDebugMacro(<< "opj_set_decode_area() after"); + +@@ -509,6 +467,5 @@ + this->m_Internal->m_Dinfo = nullptr; + opj_stream_destroy(l_stream); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl + << "Reason: opj_set_decode_area returns false"); + } +@@ -525,13 +482,14 @@ + + OPJ_UINT32 l_max_data_size = 1000; + +- bool l_go_on = true; ++ OPJ_BOOL l_go_on = true; + + auto * l_data = (OPJ_BYTE *)malloc(1000); + + while (l_go_on) + { + bool tileHeaderRead = opj_read_tile_header(this->m_Internal->m_Dinfo, ++ l_stream, + &l_tile_index, + &l_data_size, + &l_current_tile_x0, +@@ -540,13 +498,11 @@ + &l_current_tile_y1, + &l_nb_comps, +- &l_go_on, +- l_stream); ++ &l_go_on); + + if (!tileHeaderRead) + { + free(l_data); + opj_stream_destroy(l_stream); +- fclose(l_file); + opj_destroy_codec(this->m_Internal->m_Dinfo); + opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl +@@ -571,7 +527,6 @@ + if (!l_data) + { + opj_stream_destroy(l_stream); +- fclose(l_file); + opj_destroy_codec(this->m_Internal->m_Dinfo); + opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl +@@ -590,7 +545,6 @@ + { + free(l_data); + opj_stream_destroy(l_stream); +- fclose(l_file); + opj_destroy_codec(this->m_Internal->m_Dinfo); + opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl +@@ -654,7 +608,6 @@ + { + free(l_data); + opj_stream_destroy(l_stream); +- fclose(l_file); + opj_destroy_codec(this->m_Internal->m_Dinfo); + opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl +@@ -667,13 +620,11 @@ + this->m_Internal->m_Dinfo = nullptr; + opj_stream_destroy(l_stream); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl + << "Reason: error whle reading image"); + } + + /* close the byte stream */ + opj_stream_destroy(l_stream); +- fclose(l_file); + + if (this->m_Internal->m_Dinfo) + { +@@ -840,13 +791,13 @@ + + parameters.numresolution = numberOfResolutions; + +- OPJ_COLOR_SPACE color_space = CLRSPC_GRAY; ++ OPJ_COLOR_SPACE color_space = OPJ_CLRSPC_GRAY; + opj_image_cmptparm_t cmptparms[3]; + + if (this->GetNumberOfComponents() == 3) + { + +- color_space = (this->GetPixelType() == IOPixelEnum::RGB) ? CLRSPC_SRGB : CLRSPC_UNSPECIFIED; ++ color_space = (this->GetPixelType() == IOPixelEnum::RGB) ? OPJ_CLRSPC_SRGB : OPJ_CLRSPC_UNSPECIFIED; + + /* initialize image components */ + memset(&cmptparms[0], 0, 3 * sizeof(opj_image_cmptparm_t)); +@@ -864,7 +815,7 @@ + + if (this->GetNumberOfComponents() == 1) + { +- color_space = CLRSPC_GRAY; ++ color_space = OPJ_CLRSPC_GRAY; + + /* initialize image components */ + memset(&cmptparms[0], 0, sizeof(opj_image_cmptparm_t)); +@@ -941,8 +892,9 @@ + if (extension == ".j2k") + { +- cinfo = opj_create_compress(CODEC_J2K); ++ cinfo = opj_create_compress(OPJ_CODEC_J2K); + if (!cinfo) + { ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " + << this->GetFileName() << std::endl + << "Reason: opj_create_compress(CODEC_J2K) returns nullptr"); +@@ -950,9 +902,10 @@ + } + else if (extension == ".jp2") + { +- cinfo = opj_create_compress(CODEC_JP2); ++ cinfo = opj_create_compress(OPJ_CODEC_JP2); + if (!cinfo) + { ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " + << this->GetFileName() << std::endl + << "Reason: opj_create_compress(CODEC_JP2) returns nullptr"); +@@ -960,9 +913,10 @@ + } + else if (extension == ".jpt") + { +- cinfo = opj_create_compress(CODEC_JPT); ++ cinfo = opj_create_compress(OPJ_CODEC_JPT); + if (!cinfo) + { ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " + << this->GetFileName() << std::endl + << "Reason: opj_create_compress(CODEC_JPT) returns nullptr"); +@@ -970,6 +924,7 @@ + } + else + { ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl + << "Reason: unknown encode format: " << extension); + } +@@ -985,23 +940,19 @@ + + if (!opj_setup_encoder(cinfo, ¶meters, l_image)) + { ++ opj_destroy_codec(cinfo); ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl + << "Reason: opj_setup_encoder returns false"); + } + +- FILE * l_file = fopen(parameters.outfile, "wb"); +- if (!l_file) +- { +- itkExceptionMacro("JPEG2000ImageIO failed to open file for writing: " << this->GetFileName() << std::endl +- << "Reason: " +- << itksys::SystemTools::GetLastSystemError()); +- } +- + /* open a byte stream for writing */ + /* allocate memory for all tiles */ +- opj_stream_t * cio = opj_stream_create_default_file_stream(l_file, false); ++ opj_stream_t * cio = opj_stream_create_default_file_stream(parameters.outfile, false); + if (!cio) + { ++ opj_destroy_codec(cinfo); ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " + << this->GetFileName() << std::endl + << "Reason: " +@@ -1017,7 +968,8 @@ + if (!bSuccess) + { + opj_stream_destroy(cio); +- fclose(l_file); ++ opj_destroy_codec(cinfo); ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl + << "Reason: opj_start_compress returns false"); + } +@@ -1026,7 +978,8 @@ + if (!bSuccess) + { + opj_stream_destroy(cio); +- fclose(l_file); ++ opj_destroy_codec(cinfo); ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl + << "Reason: opj_encode returns false"); + } +@@ -1035,14 +988,14 @@ + if (!bSuccess) + { + opj_stream_destroy(cio); +- fclose(l_file); ++ opj_destroy_codec(cinfo); ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl + << "Reason: opj_end_compress returns false"); + } + + /* close and free the byte stream */ + opj_stream_destroy(cio); +- fclose(l_file); + + /* free remaining compression structures */ + opj_destroy_codec(cinfo); +--- a/Modules/Nonunit/Review/src/CMakeLists.txt ++++ b/Modules/Nonunit/Review/src/CMakeLists.txt +@@ -5,7 +5,7 @@ + + add_library(ITKReview ${ITKReview_SRC}) + itk_module_link_dependencies() +-target_link_libraries(ITKReview LINK_PUBLIC ${ITKTestKernel_LIBRARIES} ${ITKIOLSM_LIBRARIES} itkopenjpeg) ++target_link_libraries(ITKReview LINK_PUBLIC ${ITKTestKernel_LIBRARIES} ${ITKIOLSM_LIBRARIES} ${ITKOpenJPEG_LIBRARIES}) + itk_module_target(ITKReview) + + diff --git a/sci-libs/itk/files/itk-5.3.0-uint8.patch b/sci-libs/itk/files/itk-5.3.0-uint8.patch new file mode 100644 index 000000000..724314574 --- /dev/null +++ b/sci-libs/itk/files/itk-5.3.0-uint8.patch @@ -0,0 +1,10 @@ +--- a/Modules/Filtering/MathematicalMorphology/include/itkMathematicalMorphologyEnums.h ++++ b/Modules/Filtering/MathematicalMorphology/include/itkMathematicalMorphologyEnums.h +@@ -20,6 +20,7 @@ + + #include <iostream> + #include "ITKMathematicalMorphologyExport.h" ++#include <cstdint> + + + namespace itk diff --git a/sci-libs/itk/files/nrrdio-linking.patch b/sci-libs/itk/files/nrrdio-linking.patch deleted file mode 100644 index a549650d2..000000000 --- a/sci-libs/itk/files/nrrdio-linking.patch +++ /dev/null @@ -1,15 +0,0 @@ -Description: Link libITKNrrdIO with -lm (needed for sqrt) -Author: Steve Robbins <smr@debian.org> -Forwarded: no - ---- insighttoolkit4-4.5.0.orig/Modules/ThirdParty/NrrdIO/src/NrrdIO/CMakeLists.txt -+++ insighttoolkit4-4.5.0/Modules/ThirdParty/NrrdIO/src/NrrdIO/CMakeLists.txt -@@ -64,7 +64,7 @@ - ADD_DEFINITIONS(-DTEEM_ZLIB=1) - - ADD_LIBRARY(ITKNrrdIO ${nrrdio_SRCS} ) --TARGET_LINK_LIBRARIES(ITKNrrdIO ${ITKZLIB_LIBRARIES}) -+TARGET_LINK_LIBRARIES(ITKNrrdIO ${ITKZLIB_LIBRARIES} -lm) - - IF(ITK_LIBRARY_PROPERTIES) - SET_TARGET_PROPERTIES(ITKNrrdIO PROPERTIES ${ITK_LIBRARY_PROPERTIES}) diff --git a/sci-libs/itk/itk-4.12.0.ebuild b/sci-libs/itk/itk-4.12.0.ebuild deleted file mode 100644 index a9633748b..000000000 --- a/sci-libs/itk/itk-4.12.0.ebuild +++ /dev/null @@ -1,136 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit eutils toolchain-funcs cmake-utils python-single-r1 - -MYPN=InsightToolkit -MYP=${MYPN}-${PV} -DOC_PV=4.5.0 - -DESCRIPTION="NLM Insight Segmentation and Registration Toolkit" -HOMEPAGE="http://www.itk.org" -SRC_URI="mirror://sourceforge/${PN}/${MYP}.tar.xz - doc? ( mirror://sourceforge/${PN}/Doxygen${MYPN}-${DOC_PV}.tar.gz )" -RESTRICT="primaryuri" - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="debug doc examples +fftw itkv3compat python review cpu_flags_x86_sse2 test vtkglue" - -RDEPEND=" - dev-libs/double-conversion:0= - media-libs/libpng:0= - media-libs/tiff:0= - sci-libs/dcmtk:0= - sci-libs/hdf5:0=[cxx] - sys-libs/zlib:0= - virtual/jpeg:0= - fftw? ( sci-libs/fftw:3.0= ) - vtkglue? ( sci-libs/vtk:0=[python?] ) -" -DEPEND="${RDEPEND} - python? ( - ${PYTHON_DEPS} - >=dev-lang/swig-2.0:0 - >=dev-cpp/gccxml-0.9.0_pre20120309 - ) - doc? ( app-doc/doxygen ) -" - -REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" - -S="${WORKDIR}/${MYP}" - -PATCHES=( - "${FILESDIR}/nrrdio-linking.patch" -) - -get_memory() { - free --giga | grep Mem | cut -d ' ' -f 15 || die 'unable to get memory size' -} - -src_configure() { - sed -i \ - -e '/find_package/d' \ - Modules/ThirdParty/DoubleConversion/CMakeLists.txt || die - - local mycmakeargs=( - -DBUILD_SHARED_LIBS=ON - -DITK_USE_SYSTEM_DCMTK=ON - -DITK_USE_SYSTEM_DOUBLECONVERSION=ON - -DITK_USE_SYSTEM_HDF5=ON - -DITK_USE_SYSTEM_JPEG=ON - -DITK_USE_SYSTEM_PNG=ON - -DITK_USE_SYSTEM_SWIG=ON - -DITK_USE_SYSTEM_TIFF=ON - -DITK_USE_SYSTEM_ZLIB=ON - -DITK_BUILD_DEFAULT_MODULES=ON - -DITK_COMPUTER_MEMORY_SIZE="$(get_memory)" - -DITK_WRAP_JAVA=OFF - -DITK_WRAP_TCL=OFF - -DBUILD_TESTING=$(usex test) - -DBUILD_EXAMPLES=$(usex examples) - -DITK_USE_REVIEW=$(usex review) - -DITKV3_COMPATIBILITY=$(usex itkv3compat) - -DVNL_CONFIG_ENABLE_SSE2=$(usex cpu_flags_x86_sse2) - ) - if use fftw; then - mycmakeargs+=( - -DUSE_FFTWD=ON - -DUSE_FFTWF=ON - -DUSE_SYSTEM_FFTW=ON - -DITK_USE_SYSTEM_FFTW=ON - -DITK_WRAPPING=ON - -DITK_WRAP_double=ON - -DITK_WRAP_vector_double=ON - -DITK_WRAP_covariant_vector_double=ON - -DITK_WRAP_complex_double=ON - ) - fi - if use vtkglue; then - mycmakeargs+=( - -DModule_ITKVtkGlue=ON - ) - fi - mycmakeargs+=( - -DITK_WRAP_PYTHON=$(usex python ON OFF) - ) - - cmake-utils_src_configure -} - -src_install() { - cmake-utils_src_install - - if use examples; then - insinto /usr/share/doc/${PF}/examples - docompress -x /usr/share/doc/${PF}/examples - doins -r "${S}"/Examples/* - fi - - echo "ITK_DATA_ROOT=${EROOT%/}/usr/share/${PN}/data" > ${T}/40${PN} - local ldpath="${EROOT%/}/usr/$(get_libdir)/InsightToolkit" - if use python; then - echo "PYTHONPATH=${EROOT%/}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> "${T}"/40${PN} - ldpath="${ldpath}:${EROOT%/}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib" - fi - echo "LDPATH=${ldpath}" >> "${T}"/40${PN} - doenvd "${T}"/40${PN} - - if use doc; then - insinto /usr/share/doc/${PF}/api-docs - cd "${WORKDIR}"/html - rm *.md5 || die "Failed to remove superfluous hashes" - einfo "Installing API docs. This may take some time." - insinto /usr/share/doc/${PF}/api-docs - doins -r * - fi - - mv "${D}/usr/lib" "${D}/usr/$(get_libdir)" || \ - die 'unable to fix libdir' -} diff --git a/sci-libs/itk/itk-4.4.2-r1.ebuild b/sci-libs/itk/itk-4.4.2-r1.ebuild deleted file mode 100644 index 93a03a5f8..000000000 --- a/sci-libs/itk/itk-4.4.2-r1.ebuild +++ /dev/null @@ -1,135 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit eutils toolchain-funcs cmake-utils python-single-r1 - -MYPN=InsightToolkit -MYP=${MYPN}-${PV} - -DESCRIPTION="NLM Insight Segmentation and Registration Toolkit" -HOMEPAGE="http://www.itk.org" -SRC_URI=" - mirror://sourceforge/${PN}/${MYP}.tar.gz - doc? ( mirror://sourceforge/${PN}/Doxygen${MYPN}-4.4.0.tar.gz )" -RESTRICT="primaryuri" - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="debug doc examples fftw itkv3compat python review cpu_flags_x86_sse2 test vtkglue" - -RDEPEND=" - sci-libs/hdf5[cxx] - virtual/jpeg:0= - media-libs/libpng:0= - media-libs/tiff:0= - sys-libs/zlib - fftw? ( sci-libs/fftw:3.0 ) - vtkglue? ( sci-libs/vtk ) -" -DEPEND="${RDEPEND} - python? ( - ${PYTHON_DEPS} - >=dev-lang/swig-2.0:0 - >=dev-cpp/gccxml-0.9.0_pre20120309 - ) - doc? ( app-doc/doxygen ) -" - -S="${WORKDIR}/${MYP}" - -pkg_pretend() { - if [[ -z ${ITK_COMPUTER_MEMORY_SIZE} ]]; then - elog "To tune ITK to make the best use ouf working memory you can set" - elog " ITK_COMPUTER_MEMORY_SIZE=XX" - elog "in make.conf, default is 1 (unit is GB)" - fi - if use python && [[ -z ${ITK_WRAP_DIMS} ]]; then - elog "For Python language bindings, you can define the dimensions" - elog "you want to create bindings for by setting" - elog " ITK_WRAP_DIMS=X;Y;Z..." - elog "in make.conf, default is 2;3 for 2D and 3D data" - fi -} - -src_configure() { - local mycmakeargs=( - -DWRAP_ITK_JAVA=OFF - -DWRAP_ITK_TCL=OFF - -DITK_USE_SYSTEM_HDF5=ON - -DITK_USE_SYSTEM_JPEG=ON - -DITK_USE_SYSTEM_PNG=ON - -DITK_USE_SYSTEM_TIFF=ON - -DITK_USE_SYSTEM_ZLIB=ON - -DITK_USE_SYSTEM_GCCXML=ON - -DITK_USE_SYSTEM_SWIG=ON - -DITK_BUILD_ALL_MODULES=ON - -DBUILD_SHARED_LIBS=ON - -DBUILD_EXAMPLES=OFF - -DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}" - $(cmake-utils_use_build test TESTING) - $(cmake-utils_use review ITK_USE_REVIEW) - $(cmake-utils_use itkv3compat ITKV3_COMPATIBILITY) - $(cmake-utils_use cpu_flags_x86_sse2 VNL_CONFIG_ENABLE_SSE2) - ) - if use fftw; then - mycmakeargs+=( - -DUSE_FFTWD=ON - -DUSE_FFTWF=ON - -DUSE_SYSTEM_FFTW=ON - -DITK_WRAP_double=ON - -DITK_WRAP_vector_double=ON - -DITK_WRAP_covariant_vector_double=ON - -DITK_WRAP_complex_double=ON - ) - fi - if use vtkglue; then - mycmakeargs+=( - -DModule_ITKVtkGlue=ON - ) - fi - if use python; then - mycmakeargs+=( - -DITK_WRAP_PYTHON=ON - -DITK_WRAP_DIMS="${ITK_WRAP_DIMS:-2;3}" - ) - else - mycmakeargs+=( - -DITK_WRAP_PYTHON=OFF - ) - fi - cmake-utils_src_configure -} - -src_install() { - cmake-utils_src_install - - if use examples; then - insinto /usr/share/doc/${PF}/examples - docompress -x /usr/share/doc/${PF}/examples - doins -r "${S}"/Examples/* - fi - - echo "ITK_DATA_ROOT=${EROOT}/usr/share/${PN}/data" > ${T}/40${PN} - local ldpath="${EROOT}/usr/$(get_libdir)/InsightToolkit" - if use python; then - echo "PYTHONPATH=${EROOT}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> ${T}/40${PN} - ldpath="${ldpath}:${EROOT}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib" - fi - echo "LDPATH=${ldpath}" >> ${T}/40${PN} - - if use doc; then - insinto "/usr/share/doc/${PF}/api-docs" - cd "${WORKDIR}"/html - rm -f *.md5 || die "Failed to remove superfluous hashes" - einfo "Installing API docs. This may take some time." - insinto "/usr/share/doc/${PF}/api-docs" - doins -r ./* - fi - - doenvd "${T}"/40${PN} -} diff --git a/sci-libs/itk/itk-4.4.2.ebuild b/sci-libs/itk/itk-4.4.2.ebuild deleted file mode 100644 index 2d3b9f961..000000000 --- a/sci-libs/itk/itk-4.4.2.ebuild +++ /dev/null @@ -1,115 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit eutils toolchain-funcs cmake-utils python-single-r1 - -MYP=InsightToolkit-${PV} - -DESCRIPTION="NLM Insight Segmentation and Registration Toolkit" -HOMEPAGE="http://www.itk.org" -SRC_URI="mirror://sourceforge/${PN}/${MYP}.tar.gz" - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="debug examples fftw itkv3compat python review cpu_flags_x86_sse2 test" - -RDEPEND=" - sci-libs/hdf5[cxx] - virtual/jpeg:0= - media-libs/libpng:0= - media-libs/tiff:0= - sys-libs/zlib - fftw? ( sci-libs/fftw:3.0 ) -" -DEPEND="${RDEPEND} - python? ( - ${PYTHON_DEPS} - >=dev-lang/swig-2.0:0 - >=dev-cpp/gccxml-0.9.0_pre20120309 - ) -" - -S="${WORKDIR}/${MYP}" - -pkg_pretend() { - if [[ -z ${ITK_COMPUTER_MEMORY_SIZE} ]]; then - elog "To tune ITK to make the best use ouf working memory you can set" - elog " ITK_COMPUTER_MEMORY_SIZE=XX" - elog "in make.conf, default is 1 (unit is GB)" - fi - if use python && [[ -z ${ITK_WRAP_DIMS} ]]; then - elog "For Python language bindings, you can define the dimensions" - elog "you want to create bindings for by setting" - elog " ITK_WRAP_DIMS=X;Y;Z..." - elog "in make.conf, default is 2;3 for 2D and 3D data" - fi -} - -src_configure() { - local mycmakeargs=( - -DWRAP_ITK_JAVA=OFF - -DWRAP_ITK_TCL=OFF - -DITK_USE_SYSTEM_HDF5=ON - -DITK_USE_SYSTEM_JPEG=ON - -DITK_USE_SYSTEM_PNG=ON - -DITK_USE_SYSTEM_TIFF=ON - -DITK_USE_SYSTEM_ZLIB=ON - -DITK_USE_SYSTEM_GCCXML=ON - -DITK_USE_SYSTEM_SWIG=ON - -DITK_BUILD_ALL_MODULES=ON - -DBUILD_SHARED_LIBS=ON - -DBUILD_EXAMPLES=OFF - -DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}" - $(cmake-utils_use_build test TESTING) - $(cmake-utils_use review ITK_USE_REVIEW) - $(cmake-utils_use itkv3compat ITKV3_COMPATIBILITY) - $(cmake-utils_use cpu_flags_x86_sse2 VNL_CONFIG_ENABLE_SSE2) - ) - if use fftw; then - mycmakeargs+=( - -DUSE_FFTWD=ON - -DUSE_FFTWF=ON - -DUSE_SYSTEM_FFTW=ON - -DITK_WRAP_double=ON - -DITK_WRAP_vector_double=ON - -DITK_WRAP_covariant_vector_double=ON - -DITK_WRAP_complex_double=ON - ) - fi - if use python; then - mycmakeargs+=( - -DITK_WRAP_PYTHON=ON - -DITK_WRAP_DIMS="${ITK_WRAP_DIMS:-2;3}" - ) - else - mycmakeargs+=( - -DITK_WRAP_PYTHON=OFF - ) - fi - cmake-utils_src_configure -} - -src_install() { - cmake-utils_src_install - - if use examples; then - insinto /usr/share/doc/${PF}/examples - docompress -x /usr/share/doc/${PF}/examples - doins -r "${S}"/Examples/* - fi - - echo "ITK_DATA_ROOT=${EROOT}/usr/share/${PN}/data" > ${T}/40${PN} - local ldpath="${EROOT}/usr/$(get_libdir)/InsightToolkit" - if use python; then - echo "PYTHONPATH=${EROOT}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> ${T}/40${PN} - ldpath="${ldpath}:${EROOT}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib" - fi - echo "LDPATH=${ldpath}" >> ${T}/40${PN} - - doenvd "${T}"/40${PN} -} diff --git a/sci-libs/itk/itk-4.5.1.ebuild b/sci-libs/itk/itk-4.5.1.ebuild deleted file mode 100644 index 199c03659..000000000 --- a/sci-libs/itk/itk-4.5.1.ebuild +++ /dev/null @@ -1,155 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit eutils toolchain-funcs cmake-utils python-single-r1 - -MYPN=InsightToolkit -MYP=${MYPN}-${PV} -DOC_PV=4.5.0 - -DESCRIPTION="NLM Insight Segmentation and Registration Toolkit" -HOMEPAGE="http://www.itk.org" -SRC_URI="mirror://sourceforge/${PN}/${MYP}.tar.xz - doc? ( mirror://sourceforge/${PN}/Doxygen${MYPN}-${DOC_PV}.tar.gz )" -RESTRICT="primaryuri" - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="debug doc examples fftw itkv3compat python review cpu_flags_x86_sse2 test vtkglue" - -RDEPEND=" - dev-libs/double-conversion:0= - media-libs/libpng:0= - media-libs/tiff:0= - sci-libs/dcmtk:0= - sci-libs/hdf5:0=[cxx] - sys-libs/zlib:0= - virtual/jpeg:0= - fftw? ( sci-libs/fftw:3.0= ) - vtkglue? ( sci-libs/vtk:0=[python?] ) -" -DEPEND="${RDEPEND} - python? ( - ${PYTHON_DEPS} - >=dev-lang/swig-2.0:0 - >=dev-cpp/gccxml-0.9.0_pre20120309 - ) - doc? ( app-doc/doxygen ) -" - -REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" - -S="${WORKDIR}/${MYP}" - -PATCHES=( - "${FILESDIR}"/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch - "${FILESDIR}"/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch - "${FILESDIR}"/0003-COMP-Fixed-itkGradientDescentOptimizerv4-wrapping-wa.patch - "${FILESDIR}"/0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch - "${FILESDIR}"/0005-make-gdcm-helper-library-static.patch - "${FILESDIR}"/nrrdio-linking.patch -) - -pkg_pretend() { - if [[ -z ${ITK_COMPUTER_MEMORY_SIZE} ]]; then - elog "To tune ITK to make the best use of working memory you can set" - elog " ITK_COMPUTER_MEMORY_SIZE=XX" - elog "in make.conf, default is 1 (unit is GB)" - fi - if use python && [[ -z ${ITK_WRAP_DIMS} ]]; then - elog "For Python language bindings, you can define the dimensions" - elog "you want to create bindings for by setting" - elog " ITK_WRAP_DIMS=X;Y;Z..." - elog "in make.conf, default is 2;3 for 2D and 3D data" - fi -} - -src_configure() { - sed -i \ - -e '/find_package/d' \ - Modules/ThirdParty/DoubleConversion/CMakeLists.txt || die - - local mycmakeargs=( - -DBUILD_SHARED_LIBS=ON - -DITK_USE_SYSTEM_DCMTK=ON - -DITK_USE_SYSTEM_DOUBLECONVERSION=ON - -DITK_USE_SYSTEM_GCCXML=ON - -DITK_USE_SYSTEM_HDF5=ON - -DITK_USE_SYSTEM_JPEG=ON - -DITK_USE_SYSTEM_PNG=ON - -DITK_USE_SYSTEM_SWIG=ON - -DITK_USE_SYSTEM_TIFF=ON - -DITK_USE_SYSTEM_ZLIB=ON - -DITK_BUILD_DEFAULT_MODULES=ON - -DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}" - -DWRAP_ITK_JAVA=OFF - -DWRAP_ITK_TCL=OFF - -Ddouble-conversion_INCLUDE_DIRS="${EPREFIX}/usr/include/double-conversion" - -Ddouble-conversion_LIBRARIES="-ldouble-conversion" - $(cmake-utils_use_build test TESTING) - $(cmake-utils_use_build examples EXAMPLES) - $(cmake-utils_use review ITK_USE_REVIEW) - $(cmake-utils_use itkv3compat ITKV3_COMPATIBILITY) - $(cmake-utils_use cpu_flags_x86_sse2 VNL_CONFIG_ENABLE_SSE2) - ) - if use fftw; then - mycmakeargs+=( - -DUSE_FFTWD=ON - -DUSE_FFTWF=ON - -DUSE_SYSTEM_FFTW=ON - -DITK_WRAP_double=ON - -DITK_WRAP_vector_double=ON - -DITK_WRAP_covariant_vector_double=ON - -DITK_WRAP_complex_double=ON - ) - fi - if use vtkglue; then - mycmakeargs+=( - -DModule_ITKVtkGlue=ON - ) - fi - if use python; then - mycmakeargs+=( - -DITK_WRAP_PYTHON=ON - -DITK_WRAP_DIMS="${ITK_WRAP_DIMS:-2;3}" - ) - else - mycmakeargs+=( - -DITK_WRAP_PYTHON=OFF - ) - fi - cmake-utils_src_configure -} - -src_install() { - cmake-utils_src_install - - if use examples; then - insinto /usr/share/doc/${PF}/examples - docompress -x /usr/share/doc/${PF}/examples - doins -r "${S}"/Examples/* - fi - - echo "ITK_DATA_ROOT=${EROOT%/}/usr/share/${PN}/data" > ${T}/40${PN} - local ldpath="${EROOT%/}/usr/$(get_libdir)/InsightToolkit" - if use python; then - echo "PYTHONPATH=${EROOT%/}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> "${T}"/40${PN} - ldpath="${ldpath}:${EROOT%/}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib" - fi - echo "LDPATH=${ldpath}" >> "${T}"/40${PN} - doenvd "${T}"/40${PN} - - if use doc; then - insinto /usr/share/doc/${PF}/api-docs - cd "${WORKDIR}"/html - rm *.md5 || die "Failed to remove superfluous hashes" - einfo "Installing API docs. This may take some time." - insinto /usr/share/doc/${PF}/api-docs - doins -r * - fi -} diff --git a/sci-libs/itk/itk-5.2.1-r2.ebuild b/sci-libs/itk/itk-5.2.1-r2.ebuild new file mode 100644 index 000000000..0b1f25860 --- /dev/null +++ b/sci-libs/itk/itk-5.2.1-r2.ebuild @@ -0,0 +1,250 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +VIRTUALX_REQUIRED="manual" + +inherit cmake python-single-r1 virtualx + +MY_PN="InsightToolkit" +MY_P="${MY_PN}-${PV}" +GLI_HASH="89da9305f5750d3990ca9fd35ecc5ce0b39c71a6" +IAD_HASH="24825c8d246e941334f47968553f0ae388851f0c" +TEST_HASH="7ab9d41ad5b42ccbe8adcaf0b24416d439a264d0" +declare -a GLI_TEST_HASHES=( + "a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a" + "bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f" +) + +GLI_TEST_SRC="" +for i in "${GLI_TEST_HASHES[@]}"; do + GLI_TEST_SRC+="https://data.kitware.com/api/v1/file/hashsum/sha512/${i}/download -> ${PN}-test-${i} " +done + +DESCRIPTION="NLM Insight Segmentation and Registration Toolkit" +HOMEPAGE="https://itk.org" +SRC_URI=" + https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/${MY_P}.tar.gz + https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/archive/${GLI_HASH}.tar.gz -> ITKGenericLabelInterpolator-${PV}.tar.gz + https://github.com/ntustison/ITKAdaptiveDenoising/archive/${IAD_HASH}.tar.gz -> ITKAdaptiveDenoising-${PV}.tar.gz + test? ( + https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/InsightData-${PV}.tar.gz + https://github.com/InsightSoftwareConsortium/ITKTestingData/archive/${TEST_HASH}.tar.gz -> ${P}-testingdata.tar.gz + ${GLI_TEST_SRC} + ) + " + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="debug doc examples fftw itkv4-compat python review test vtkglue" +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +RESTRICT="!test? ( test )" + +RDEPEND=" + dev-cpp/eigen:3 + dev-libs/double-conversion:0= + dev-libs/expat:0= + media-libs/openjpeg:2 + media-libs/libpng:0= + media-libs/tiff:0=[jpeg] + sci-libs/dcmtk:0= + sci-libs/hdf5:0=[cxx] + sci-libs/gdcm:0= + sys-libs/zlib:0= + media-libs/libjpeg-turbo:0= + fftw? ( sci-libs/fftw:3.0= ) + vtkglue? ( + sci-libs/vtk:0=[rendering] + python? ( + sci-libs/vtk:0=[python,${PYTHON_SINGLE_USEDEP}] + ) + ) + python? ( ${PYTHON_DEPS} ) +" +DEPEND="${RDEPEND} + sys-apps/coreutils + python? ( + >=dev-lang/swig-2.0:0 + dev-libs/castxml + ) + doc? ( app-text/doxygen ) +" +BDEPEND=" + test? ( + vtkglue? ( ${VIRTUALX_DEPEND} ) + python? ( + $(python_gen_cond_dep 'dev-python/numpy[${PYTHON_USEDEP}]') + ) + ) +" + +S="${WORKDIR}/${MY_P}" + +PATCHES=( + "${FILESDIR}/${P}-upstream-fixes.patch" + "${FILESDIR}/${P}-system-tiff-has-64.patch" + "${FILESDIR}/${P}-fix-castxml-clang-attr-malloc.patch" + "${FILESDIR}/${P}-system-openjpeg.patch" +) + +pkg_pretend() { + if [[ -z ${ITK_COMPUTER_MEMORY_SIZE} ]]; then + elog "To tune ITK to make the best use of working memory you can set" + elog " ITK_COMPUTER_MEMORY_SIZE=XX" + elog "in make.conf, default is 1 (unit is GB)" + fi + if use python && [[ -z ${ITK_WRAP_DIMS} ]]; then + elog "For Python language bindings, you can define the dimensions" + elog "you want to create bindings for by setting" + elog " ITK_WRAP_DIMS=X;Y;Z..." + elog "in make.conf, default is 2;3 for 2D and 3D data" + fi +} + +src_prepare() { + # drop bundled libs + local -a DROPS=( + DoubleConversion/src/double-conversion + Eigen3/src/itkeigen + Expat/src/expat + GDCM/src/gdcm + JPEG/src/itkjpeg + HDF5/src/itkhdf5 + OpenJPEG/src/openjpeg + PNG/src/itkpng + TIFF/src/itktiff + ZLIB/src/itkzlib + ) + local x + for x in "${DROPS[@]}"; do + ebegin "Dropping bundled ${x%%/*}" + rm -r "Modules/ThirdParty/${x}" || die + eend $? + done + { + find Modules/ThirdParty -mindepth 2 -maxdepth 2 -type d -name src -printf '%P\n' + printf '%s\n' "${DROPS[@]}" | sed 's,/[^/]*$,,' + } | sort | uniq -u | xargs -n 1 ewarn "Using bundled" || die + + # Remote modules + ln -sr "../ITKGenericLabelInterpolator-${GLI_HASH}" Modules/External/ITKGenericLabelInterpolator || die + ln -sr "../ITKAdaptiveDenoising-${IAD_HASH}" Modules/External/ITKAdaptiveDenoising || die + + cmake_src_prepare + + if use test; then + cp -rf "../ITKTestingData-${TEST_HASH}/"* ".ExternalData/" || die + mv "../ITKTestingData-${TEST_HASH}" "${BUILD_DIR}/.ExternalData" || die + for i in "${GLI_TEST_HASHES[@]}"; do + cp "${DISTDIR}/${PN}-test-${i}" ".ExternalData/SHA512/${i}" || die + cp "${DISTDIR}/${PN}-test-${i}" "${BUILD_DIR}/.ExternalData/SHA512/${i}" || die + done + fi +} + +src_configure() { + local mycmakeargs=( + -DITK_BUILD_DOCUMENTATION="$(usex doc ON OFF)" + -DITK_INSTALL_DOC_DIR="share/doc/${P}" + -DBUILD_EXAMPLES="$(usex examples ON OFF)" + -DBUILD_SHARED_LIBS=ON + -DBUILD_TESTING="$(usex test ON OFF)" + -Ddouble-conversion_INCLUDE_DIRS="${EPREFIX}/usr/include/double-conversion" + -DExternalData_OBJECT_STORES="${WORKDIR}/InsightToolkit-${PV}/.ExternalData" + -DGDCM_USE_SYSTEM_OPENJPEG=ON + -DITK_FORBID_DOWNLOADS:BOOL=ON + -DITK_INSTALL_LIBRARY_DIR=$(get_libdir) + -DITK_USE_REVIEW="$(usex review ON OFF)" + -DITK_USE_SYSTEM_DCMTK=ON + -DITK_USE_SYSTEM_DOUBLECONVERSION=ON + -DITK_USE_SYSTEM_CASTXML=ON + -DITK_USE_SYSTEM_EIGEN=ON + -DITK_USE_SYSTEM_EXPAT=ON + -DITK_USE_SYSTEM_GDCM=ON + -DITK_USE_SYSTEM_HDF5=ON + -DITK_USE_SYSTEM_JPEG=ON + -DITK_USE_SYSTEM_OPENJPEG=ON + -DITK_USE_SYSTEM_PNG=ON + -DITK_USE_SYSTEM_SWIG=ON + -DITK_USE_SYSTEM_TIFF=ON + -DITK_USE_SYSTEM_ZLIB=ON + -DITK_USE_KWSTYLE=OFF + -DITK_BUILD_DEFAULT_MODULES=ON + -DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}" + -DModule_AdaptiveDenoising:BOOL=ON + -DModule_GenericLabelInterpolator:BOOL=ON + -DModule_ITKReview:BOOL=ON + -DWRAP_ITK_JAVA=OFF + -DWRAP_ITK_TCL=OFF + -DITKV4_COMPATIBILITY:BOOL=$(usex itkv4-compat) + ) + if use fftw; then + mycmakeargs+=( + -DUSE_FFTWD=ON + -DUSE_FFTWF=ON + -DUSE_SYSTEM_FFTW=ON + -DITK_WRAP_double=ON + -DITK_WRAP_vector_double=ON + -DITK_WRAP_covariant_vector_double=ON + -DITK_WRAP_complex_double=ON + ) + fi + if use vtkglue; then + mycmakeargs+=( + -DModule_ITKVtkGlue=ON + ) + fi + if use python; then + mycmakeargs+=( + -DITK_WRAP_PYTHON=ON + -DPython3_EXECUTABLE="${PYTHON}" + -DITK_WRAP_DIMS="${ITK_WRAP_DIMS:-2;3}" + ) + else + mycmakeargs+=( + -DITK_WRAP_PYTHON=OFF + ) + fi + cmake_src_configure +} + +src_install() { + cmake_src_install + + if use examples; then + docinto examples + docompress -x /usr/share/doc/${PF}/examples + dodoc -r "${S}"/Examples/* + fi + + echo "ITK_DATA_ROOT=${EPREFIX}/usr/share/${PN}/data" > ${T}/40${PN} || die + local ldpath="${EPREFIX}/usr/$(get_libdir)/InsightToolkit" + if use python; then + echo "PYTHONPATH=${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> "${T}"/40${PN} || die + ldpath="${ldpath}:${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib" + fi + echo "LDPATH=${ldpath}" >> "${T}"/40${PN} || die + doenvd "${T}"/40${PN} + + if use doc; then + cd "${WORKDIR}"/html || die + rm *.md5 || die "Failed to remove superfluous hashes" + einfo "Installing API docs. This may take some time." + docinto api-docs + dodoc -r * + fi + + use python && python_optimize +} + +src_test() { + if use vtkglue; then + virtx cmake_src_test + else + cmake_src_test + fi +} diff --git a/sci-libs/itk/itk-5.3.0-r1.ebuild b/sci-libs/itk/itk-5.3.0-r1.ebuild new file mode 100644 index 000000000..b2c3af801 --- /dev/null +++ b/sci-libs/itk/itk-5.3.0-r1.ebuild @@ -0,0 +1,269 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +VIRTUALX_REQUIRED="manual" + +inherit cmake python-single-r1 virtualx + +MY_PN="InsightToolkit" +MY_P="${MY_PN}-${PV}" +GLI_V="1.2.0" +IAD_HASH="24825c8d246e941334f47968553f0ae388851f0c" +TEST_HASH="bb6d3b9a932333901465c75417fe8859124f5fed" +declare -a GLI_TEST_HASHES=( + "a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a" + "bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f" +) + +GLI_TEST_SRC="" +for i in "${GLI_TEST_HASHES[@]}"; do + GLI_TEST_SRC+="https://data.kitware.com/api/v1/file/hashsum/sha512/${i}/download -> ${PN}-test-${i} " +done + +DESCRIPTION="NLM Insight Segmentation and Registration Toolkit" +HOMEPAGE="https://itk.org" +SRC_URI=" + https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/${MY_P}.tar.gz + https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/archive/refs/tags/v${GLI_V}.tar.gz -> ITKGenericLabelInterpolator-${GLI_V}.tar.gz + https://github.com/ntustison/ITKAdaptiveDenoising/archive/${IAD_HASH}.tar.gz -> ITKAdaptiveDenoising-${PV}.tar.gz + test? ( + https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/InsightData-${PV}.tar.gz + https://github.com/InsightSoftwareConsortium/ITKTestingData/archive/${TEST_HASH}.tar.gz -> ${P}-testingdata.tar.gz + ${GLI_TEST_SRC} + ) + " + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="debug doc examples fftw itkv4-compat python review test vtkglue" +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +RESTRICT="!test? ( test )" + +RDEPEND=" + dev-cpp/eigen:3 + dev-libs/double-conversion:0= + dev-libs/expat:0= + dev-libs/icu:0= + media-libs/libjpeg-turbo:0= + media-libs/libpng:0= + media-libs/openjpeg:2 + media-libs/tiff:0=[jpeg] + sci-libs/dcmtk:0= + sci-libs/gdcm:0= + sci-libs/hdf5:0=[cxx] + sys-libs/zlib-ng + fftw? ( sci-libs/fftw:3.0=[threads] ) + vtkglue? ( + sci-libs/vtk:0=[rendering] + python? ( + sci-libs/vtk:0=[python,${PYTHON_SINGLE_USEDEP}] + ) + ) + python? ( ${PYTHON_DEPS} ) +" +# Might also need: +# dev-libs/kwsys::guru +# kwiml +# minc +# metaio +# niftilib +# sci-lib/vxl::science +DEPEND="${RDEPEND} + sys-apps/coreutils + python? ( + >=dev-lang/swig-2.0:0 + dev-libs/castxml + ) + doc? ( app-text/doxygen ) +" +BDEPEND=" + test? ( + vtkglue? ( ${VIRTUALX_DEPEND} ) + python? ( + $(python_gen_cond_dep 'dev-python/numpy[${PYTHON_USEDEP}]') + ) + ) +" + +S="${WORKDIR}/${MY_P}" + +# uint patch applied by upstream for next release. +PATCHES=( + "${FILESDIR}/${PN}-5.2.1-system-tiff-has-64.patch" + "${FILESDIR}/${PN}-5.3.0-system-openjpeg.patch" + "${FILESDIR}/${PN}-5.3.0-uint8.patch" +) + +pkg_pretend() { + if [[ -z ${ITK_COMPUTER_MEMORY_SIZE} ]]; then + elog "To tune ITK to make the best use of working memory you can set" + elog " ITK_COMPUTER_MEMORY_SIZE=XX" + elog "in make.conf, default is 1 (unit is GB)" + fi + if use python && [[ -z ${ITK_WRAP_DIMS} ]]; then + elog "For Python language bindings, you can define the dimensions" + elog "you want to create bindings for by setting" + elog " ITK_WRAP_DIMS=X;Y;Z..." + elog "in make.conf, default is 2;3 for 2D and 3D data" + fi +} + +src_prepare() { + # drop bundled libs + local -a DROPS=( + DoubleConversion/src/double-conversion + Eigen3/src/itkeigen + Expat/src/expat + GDCM/src/gdcm + JPEG/src/itkjpeg + HDF5/src/itkhdf5 + OpenJPEG/src/openjpeg + PNG/src/itkpng + TIFF/src/itktiff + ZLIB/src/itkzlib-ng + ) + local x + for x in "${DROPS[@]}"; do + ebegin "Dropping bundled ${x%%/*}" + rm -r "Modules/ThirdParty/${x}" || die + eend $? + done + { + find Modules/ThirdParty -mindepth 2 -maxdepth 2 -type d -name src -printf '%P\n' + printf '%s\n' "${DROPS[@]}" | sed 's,/[^/]*$,,' + } | sort | uniq -u | xargs -n 1 ewarn "Using bundled" || die + + # Remote modules + ln -sr "../ITKGenericLabelInterpolator-${GLI_V}" Modules/External/ITKGenericLabelInterpolator || die + ln -sr "../ITKAdaptiveDenoising-${IAD_HASH}" Modules/External/ITKAdaptiveDenoising || die + + cmake_src_prepare + + if use test; then + cp -rf "../ITKTestingData-${TEST_HASH}/"* ".ExternalData/" || die + mv "../ITKTestingData-${TEST_HASH}" "${BUILD_DIR}/.ExternalData" || die + for i in "${GLI_TEST_HASHES[@]}"; do + cp "${DISTDIR}/${PN}-test-${i}" ".ExternalData/SHA512/${i}" || die + cp "${DISTDIR}/${PN}-test-${i}" "${BUILD_DIR}/.ExternalData/SHA512/${i}" || die + done + fi +} + +src_configure() { + local mycmakeargs=( + -DITK_BUILD_DOCUMENTATION="$(usex doc ON OFF)" + -DITK_INSTALL_DOC_DIR="share/doc/${P}" + -DBUILD_EXAMPLES="$(usex examples ON OFF)" + -DBUILD_SHARED_LIBS=ON + -DBUILD_TESTING="$(usex test ON OFF)" + -Ddouble-conversion_INCLUDE_DIRS="${EPREFIX}/usr/include/double-conversion" + -DExternalData_OBJECT_STORES="${WORKDIR}/InsightToolkit-${PV}/.ExternalData" + -DGDCM_USE_SYSTEM_OPENJPEG=ON + -DITK_FORBID_DOWNLOADS:BOOL=ON + -DITK_INSTALL_LIBRARY_DIR=$(get_libdir) + -DITK_USE_REVIEW="$(usex review ON OFF)" + -DITK_USE_SYSTEM_ICU=ON + -DITK_USE_SYSTEM_DCMTK=ON + -DITK_USE_SYSTEM_DOUBLECONVERSION=ON + -DITK_USE_SYSTEM_CASTXML=ON + -DITK_USE_SYSTEM_EIGEN=ON + -DITK_USE_SYSTEM_EXPAT=ON + -DITK_USE_SYSTEM_GDCM=ON + -DITK_USE_SYSTEM_HDF5=ON + -DITK_USE_SYSTEM_JPEG=ON + -DITK_USE_SYSTEM_OPENJPEG=ON + -DITK_USE_SYSTEM_PNG=ON + -DITK_USE_SYSTEM_SWIG=ON + -DITK_USE_SYSTEM_TIFF=ON + -DITK_USE_SYSTEM_ZLIB=ON + -DITK_USE_KWSTYLE=OFF + -DITK_BUILD_DEFAULT_MODULES=ON + -DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}" + -DModule_AdaptiveDenoising:BOOL=ON + -DModule_GenericLabelInterpolator:BOOL=ON + -DModule_ITKReview:BOOL=ON + -DWRAP_ITK_JAVA=OFF + -DWRAP_ITK_TCL=OFF + -DITKV4_COMPATIBILITY:BOOL=$(usex itkv4-compat) + ) + if use fftw; then + mycmakeargs+=( + -DITK_USE_FFTWD:BOOL=ON + -DITK_USE_FFTWF:BOOL=ON + -DITK_USE_SYSTEM_FFTW:BOOL=ON + -DITK_WRAP_double=ON + -DITK_WRAP_vector_double=ON + -DITK_WRAP_covariant_vector_double=ON + -DITK_WRAP_complex_double=ON + ) + else + mycmakeargs+=( + -DITK_USE_FFTWD:BOOL=OFF + -DITK_USE_FFTWF:BOOL=OFF + -DITK_USE_SYSTEM_FFTW:BOOL=OFF + -DITK_WRAP_double=OFF + -DITK_WRAP_vector_double=OFF + -DITK_WRAP_covariant_vector_double=OFF + -DITK_WRAP_complex_double=OFF + ) + fi + if use vtkglue; then + mycmakeargs+=( + -DModule_ITKVtkGlue=ON + ) + fi + if use python; then + mycmakeargs+=( + -DITK_WRAP_PYTHON=ON + -DPython3_EXECUTABLE="${PYTHON}" + -DITK_WRAP_DIMS="${ITK_WRAP_DIMS:-2;3}" + ) + else + mycmakeargs+=( + -DITK_WRAP_PYTHON=OFF + ) + fi + cmake_src_configure +} + +src_install() { + cmake_src_install + + if use examples; then + docinto examples + docompress -x /usr/share/doc/${PF}/examples + dodoc -r "${S}"/Examples/* + fi + + echo "ITK_DATA_ROOT=${EPREFIX}/usr/share/${PN}/data" > ${T}/40${PN} || die + local ldpath="${EPREFIX}/usr/$(get_libdir)/InsightToolkit" + if use python; then + echo "PYTHONPATH=${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> "${T}"/40${PN} || die + ldpath="${ldpath}:${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib" + fi + echo "LDPATH=${ldpath}" >> "${T}"/40${PN} || die + doenvd "${T}"/40${PN} + + if use doc; then + cd "${WORKDIR}"/html || die + rm *.md5 || die "Failed to remove superfluous hashes" + einfo "Installing API docs. This may take some time." + docinto api-docs + dodoc -r * + fi + + use python && python_optimize +} + +src_test() { + if use vtkglue; then + virtx cmake_src_test + else + cmake_src_test + fi +} diff --git a/sci-libs/itk/metadata.xml b/sci-libs/itk/metadata.xml index 8485fb7e1..5da2678ec 100644 --- a/sci-libs/itk/metadata.xml +++ b/sci-libs/itk/metadata.xml @@ -9,16 +9,17 @@ <name>Gentoo Biology Project</name> </maintainer> <longdescription lang="en"> -Insight Segmentation and Registration Toolkit (ITK) is a library -that provides developers with an extensive suite of tools for image -analysis. -</longdescription> - <use> - <flag name="itkv3compat">Enable compatibility with ITK version 3</flag> + Insight Segmentation and Registration Toolkit (ITK) is a library + that provides developers with an extensive suite of tools for image + analysis. + </longdescription> + <use> + <flag name="itkv4-compat">Compatibility for applications using ITKv4 API</flag> <flag name="review">Enable compilation of methods under review</flag> <flag name="vtkglue">PLEASE FIX MY DESCRIPTION</flag> </use> <upstream> + <remote-id type="github">InsightSoftwareConsortium/ITK</remote-id> <remote-id type="sourceforge">itk</remote-id> </upstream> </pkgmetadata> |