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ITK 5 version bump ahead of Gentoo Science

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This commit is contained in:
Horea Christian 2019-03-26 00:02:13 +01:00
parent 650cb4178d
commit 11a278cd88
9 changed files with 369 additions and 0 deletions
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1
sci-libs/itk/Manifest Normal file
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DIST v5.0rc01.tar.gz 20944543 SHA256 fa6cd61bc39ccdc53808b9b0df5dd95d63a3c08be130e63ab0f4b77ca9594e46 SHA512 30e327708c7717bb2131911c86802c4104730d146b4263c68ae89384d3f01a6675b3abf5962af14cc7f40984cb1e8eedd911fe0f084a8deb4c79b4239b309728 WHIRLPOOL 6447eccbb17573233f750e3462dadd4c44c177613ca88520787579cc6e10ac523488e44dbf0f3e690a0cc009443b5adccdf62b588bdf6180dbda4a98b7d03cef

50
sci-libs/itk/files/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch Normal file
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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

28
sci-libs/itk/files/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch Normal file
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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

73
sci-libs/itk/files/0003-COMP-Fixed-itkGradientDescentOptimizerv4-wrapping-wa.patch Normal file
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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

30
sci-libs/itk/files/0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch Normal file
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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()

11
sci-libs/itk/files/0005-make-gdcm-helper-library-static.patch Normal file
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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()

15
sci-libs/itk/files/nrrdio-linking.patch Normal file
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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})

137
sci-libs/itk/itk-5.0_rc1.ebuild Normal file
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# 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
MY_PV="5.0rc01"
DESCRIPTION="NLM Insight Segmentation and Registration Toolkit"
HOMEPAGE="http://www.itk.org"
SRC_URI="https://github.com/InsightSoftwareConsortium/ITK/archive/v${MY_PV}.tar.gz"
RESTRICT="primaryuri"
LICENSE="Apache-2.0"
SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
IUSE="debug doc examples fftw itkv3compat python review test vtkglue"
RDEPEND="
dev-libs/double-conversion:0=
media-libs/libpng:0=
media-libs/tiff:0=
sci-libs/dcmtk:0=
sci-libs/hdf5:0=[cxx]
sys-libs/zlib:0=
virtual/jpeg:0=
fftw? ( sci-libs/fftw:3.0= )
vtkglue? ( sci-libs/vtk:0=[python?] )
"
DEPEND="${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}/ITK-${MY_PV}"
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 ${ITK_WRAP_DIMS} ]]; then
elog "For Python language bindings, you can define the dimensions"
elog "you want to create bindings for by setting"
elog " ITK_WRAP_DIMS=X;Y;Z..."
elog "in make.conf, default is 2;3 for 2D and 3D data"
fi
}
src_configure() {
local mycmakeargs=(
-DBUILD_SHARED_LIBS=ON
-DITK_USE_SYSTEM_DCMTK=ON
-DITK_USE_SYSTEM_DOUBLECONVERSION=ON
-DITK_USE_SYSTEM_GCCXML=ON
-DITK_USE_SYSTEM_HDF5=ON
-DITK_USE_SYSTEM_JPEG=ON
-DITK_USE_SYSTEM_PNG=ON
-DITK_USE_SYSTEM_SWIG=ON
-DITK_USE_SYSTEM_TIFF=ON
-DITK_USE_SYSTEM_ZLIB=ON
-DITK_BUILD_DEFAULT_MODULES=ON
-DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}"
-DWRAP_ITK_JAVA=OFF
-DWRAP_ITK_TCL=OFF
-Ddouble-conversion_INCLUDE_DIRS="${EPREFIX}/usr/include/double-conversion"
$(cmake-utils_use_build test TESTING)
$(cmake-utils_use_build examples EXAMPLES)
$(cmake-utils_use review ITK_USE_REVIEW)
$(cmake-utils_use itkv3compat ITKV3_COMPATIBILITY)
)
if use fftw; then
mycmakeargs+=(
-DUSE_FFTWD=ON
-DUSE_FFTWF=ON
-DUSE_SYSTEM_FFTW=ON
-DITK_WRAP_double=ON
-DITK_WRAP_vector_double=ON
-DITK_WRAP_covariant_vector_double=ON
-DITK_WRAP_complex_double=ON
)
fi
if use vtkglue; then
mycmakeargs+=(
-DModule_ITKVtkGlue=ON
)
fi
if use python; then
mycmakeargs+=(
-DITK_WRAP_PYTHON=ON
-DITK_WRAP_DIMS="${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
}

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sci-libs/itk/metadata.xml Normal file
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<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>maintainer-wanted@gentoo.org</email>
</maintainer>
<maintainer type="project">
<email>sci-biology@gentoo.org</email>
<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>
<flag name="review">Enable compilation of methods under review</flag>
<flag name="vtkglue">PLEASE FIX MY DESCRIPTION</flag>
</use>
<upstream>
<remote-id type="sourceforge">itk</remote-id>
</upstream>
</pkgmetadata>