* [gentoo-commits] proj/sci:master commit in: sci-libs/itk/, sci-libs/itk/files/
@ 2019-09-09 8:26 Horea Christian
0 siblings, 0 replies; 8+ messages in thread
From: Horea Christian @ 2019-09-09 8:26 UTC (permalink / raw
To: gentoo-commits
commit: 445eb95b61c9b12481b24f962123d0f13e940ab6
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Mon Sep 9 08:25:49 2019 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Sep 9 08:25:49 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=445eb95b
sci-libs/itk: version bump to 5.0.1
And removed deprecated versions on account of gccxml removal
Package-Manager: Portage-2.3.72, Repoman-2.3.17
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-libs/itk/files/ITKModuleRemote.patch | 45 ++++++
sci-libs/itk/files/tests.patch | 41 ++++++
sci-libs/itk/itk-4.12.0.ebuild | 136 ------------------
sci-libs/itk/itk-4.4.2-r1.ebuild | 135 ------------------
sci-libs/itk/itk-4.4.2.ebuild | 115 ---------------
sci-libs/itk/itk-4.5.1.ebuild | 155 ---------------------
.../itk/{itk-5.0_rc1.ebuild => itk-5.0.1.ebuild} | 50 +++++--
sci-libs/itk/metadata.xml | 1 -
8 files changed, 124 insertions(+), 554 deletions(-)
diff --git a/sci-libs/itk/files/ITKModuleRemote.patch b/sci-libs/itk/files/ITKModuleRemote.patch
new file mode 100644
index 000000000..eb130159a
--- /dev/null
+++ b/sci-libs/itk/files/ITKModuleRemote.patch
@@ -0,0 +1,45 @@
+Disable automatic git clone attempt for modules:
+https://github.com/InsightSoftwareConsortium/ITK/issues/1157
+
+--- a/CMake/ITKModuleRemote.cmake 2019-08-13 18:10:33.385472767 +0200
++++ b/CMake/ITKModuleRemote.cmake 2019-08-13 18:12:04.020198966 +0200
+@@ -165,39 +165,4 @@
+ set(Module_${_name} ON CACHE FORCE "${_description}")
+ endif()
+
+- if(Module_${_name})
+- itk_download_attempt_check(Module_${_name})
+- include(CMakeParseArguments)
+- cmake_parse_arguments(_fetch_options "" "GIT_REPOSITORY;GIT_TAG" "" ${ARGN})
+- find_package(Git)
+- if(NOT GIT_EXECUTABLE)
+- message(FATAL_ERROR "error: could not find git for clone of ${_name}")
+- endif()
+- execute_process(
+- COMMAND "${GIT_EXECUTABLE}" --version
+- OUTPUT_VARIABLE ov
+- OUTPUT_STRIP_TRAILING_WHITESPACE
+- )
+- string(REGEX REPLACE "^git version (.+)$" "\\1" _version "${ov}")
+- if("${_version}" VERSION_LESS 1.6.6)
+- message(FATAL_ERROR "Git version 1.6.6 or later is required.")
+- endif()
+-
+- set(REMOTE_GIT_TAG "${_fetch_options_GIT_TAG}")
+-
+- if( DEFINED REMOTE_GIT_TAG_${_name} AND NOT "${REMOTE_GIT_TAG_${_name}}" STREQUAL "${_fetch_options_GIT_TAG}")
+- set(REMOTE_GIT_TAG "${REMOTE_GIT_TAG_${_name}}")
+- message(STATUS "NOTE: Using override 'REMOTE_GIT_TAG_${_name}=${REMOTE_GIT_TAG}'\n"
+- " instead of value 'GIT_TAG=${_fetch_options_GIT_TAG}'\n"
+- " specified in file ${ITK_SOURCE_DIR}/Modules/Remote/${_name}.remote.cmake'")
+- endif()
+- set(REMOTE_GIT_TAG_${_name} "${REMOTE_GIT_TAG}" CACHE STRING "Override default GIT_TAG value for remote module ${_name}")
+- mark_as_advanced(REMOTE_GIT_TAG_${_name})
+-
+- _fetch_with_git("${GIT_EXECUTABLE}"
+- "${_fetch_options_GIT_REPOSITORY}"
+- "${REMOTE_GIT_TAG}"
+- "${ITK_SOURCE_DIR}/Modules/Remote/${_name}"
+- )
+- endif()
+ endfunction()
diff --git a/sci-libs/itk/files/tests.patch b/sci-libs/itk/files/tests.patch
new file mode 100644
index 000000000..c24714e4d
--- /dev/null
+++ b/sci-libs/itk/files/tests.patch
@@ -0,0 +1,41 @@
+Known to fail by upstream:
+https://github.com/InsightSoftwareConsortium/ITK/issues/1212#issuecomment-527998115
+
+--- a/Modules/Bridge/VtkGlue/test/CMakeLists.txt 2019-09-09 00:45:14.736032139 +0200
++++ b/Modules/Bridge/VtkGlue/test/CMakeLists.txt 2019-09-09 00:49:42.183935497 +0200
+@@ -7,8 +7,6 @@
+ if(NOT VTK_RENDERING_BACKEND STREQUAL "None")
+ list(APPEND ITKVtkGlueTests
+ itkVtkMedianFilterTest.cxx
+- itkVtkConnectedComponentImageFilterTest.cxx
+- QuickViewTest.cxx
+ # ### runViewImage ###
+ # No test generated. Use it for view images (2D or 3D) with:
+ # ITKVtkGlueTestDriver runViewImage image_file
+@@ -40,26 +38,3 @@
+ NAME itkVTKImageToImageFilterTest
+ COMMAND ITKVtkGlueTestDriver
+ itkVTKImageToImageFilterTest)
+-
+-if(NOT VTK_RENDERING_BACKEND STREQUAL "None")
+- itk_add_test(
+- NAME itkVtkMedianImageFilterTest
+- COMMAND ITKVtkGlueTestDriver
+- itkVtkMedianFilterTest DATA{${ITK_DATA_ROOT}/Input/cthead1.png} 2)
+- set_property(TEST itkVtkMedianImageFilterTest APPEND PROPERTY LABELS REQUIRES_DISPLAY)
+-
+- itk_add_test(
+- NAME QuickViewTest
+- COMMAND ITKVtkGlueTestDriver
+- --compare DATA{Baseline/QuickViewTest.png,:}
+- ${ITK_TEST_OUTPUT_DIR}/QuickViewTest0.png
+- --compareNumberOfPixelsTolerance 1500
+- QuickViewTest DATA{${ITK_DATA_ROOT}/Input/peppers.png} ${ITK_TEST_OUTPUT_DIR})
+- set_property(TEST QuickViewTest APPEND PROPERTY LABELS REQUIRES_DISPLAY)
+-
+- itk_add_test(
+- NAME itkVtkConnectedComponentImageFilterTest
+- COMMAND ITKVtkGlueTestDriver
+- itkVtkConnectedComponentImageFilterTest DATA{${ITK_DATA_ROOT}/Input/cthead1.png})
+- set_property(TEST itkVtkConnectedComponentImageFilterTest APPEND PROPERTY LABELS REQUIRES_DISPLAY)
+-endif()
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/${PF}/api-docs
- doins -r *
- fi
-}
diff --git a/sci-libs/itk/itk-5.0_rc1.ebuild b/sci-libs/itk/itk-5.0.1.ebuild
similarity index 69%
rename from sci-libs/itk/itk-5.0_rc1.ebuild
rename to sci-libs/itk/itk-5.0.1.ebuild
index f6433e551..e1ec7166a 100644
--- a/sci-libs/itk/itk-5.0_rc1.ebuild
+++ b/sci-libs/itk/itk-5.0.1.ebuild
@@ -1,19 +1,26 @@
# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
PYTHON_COMPAT=( python2_7 python3_{5,6,7} )
-inherit eutils toolchain-funcs cmake-utils python-single-r1
+inherit toolchain-funcs cmake-utils python-single-r1
-MY_PV="5.0rc01"
+MY_PN="InsightToolkit"
+MY_P="${MY_PN}-${PV}"
+GLI_HASH="187ab99b7d42718c99e5017f0acd3900d7469bd1"
+GLI_TEST_HASH="57b5d5de8d777f10f269445a"
DESCRIPTION="NLM Insight Segmentation and Registration Toolkit"
HOMEPAGE="http://www.itk.org"
SRC_URI="
- https://github.com/InsightSoftwareConsortium/ITK/archive/v${MY_PV}.tar.gz
- test? ( https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.0rc01/InsightData-${MY_PV}.tar.gz )
+ https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/${MY_P}.tar.gz
+ https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/archive/${GLI_HASH}.zip -> ITKGenericLabelInterpolator-${PV}.zip
+ test? (
+ https://data.kitware.com/api/v1/folder/${GLI_TEST_HASH}/download -> ITKGenericLabelInterpolator_test-${PV}.zip
+ https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/InsightData-${PV}.tar.gz
+ )
"
RESTRICT="primaryuri"
@@ -21,6 +28,9 @@ LICENSE="Apache-2.0"
SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
IUSE="debug doc examples fftw python review test vtkglue"
+# python will not work, this is a know issue upstream:
+# https://github.com/InsightSoftwareConsortium/ITK/issues/1229
+# https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/issues/10
RDEPEND="
dev-libs/double-conversion:0=
@@ -32,20 +42,25 @@ RDEPEND="
sys-libs/zlib:0=
virtual/jpeg:0=
fftw? ( sci-libs/fftw:3.0= )
- vtkglue? ( sci-libs/vtk:0=[python?] )
+ vtkglue? ( sci-libs/vtk:0=[rendering,python?] )
"
DEPEND="${RDEPEND}
+ sys-apps/coreutils
python? (
- ${PYTHON_DEPS}
>=dev-lang/swig-2.0:0
- >=dev-cpp/gccxml-0.9.0_pre20120309
+ dev-cpp/castxml
)
doc? ( app-doc/doxygen )
"
REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-S="${WORKDIR}/ITK-${MY_PV}"
+S="${WORKDIR}/${MY_P}"
+
+PATCHES=(
+ "${FILESDIR}"/ITKModuleRemote.patch
+ "${FILESDIR}"/tests.patch
+)
pkg_pretend() {
if [[ -z ${ITK_COMPUTER_MEMORY_SIZE} ]]; then
@@ -64,14 +79,23 @@ pkg_pretend() {
src_prepare() {
sed -i -e "s/find_package(OpenJPEG 2.0.0/find_package(OpenJPEG/g"\
Modules/ThirdParty/GDCM/src/gdcm/CMakeLists.txt
- default
+ ln -sr ../ITKGenericLabelInterpolator-* Modules/Remote/ITKGenericLabelInterpolator || die
+ if use test; then
+ for filename in ../GenericLabelInterpolator/test/*/*mha; do
+ MD5=$(md5sum $filename) || die
+ MD5=${MD5% *} || die
+ cp "$filename" ".ExternalData/MD5/${MD5}" || die
+ done
+ fi
+ cmake-utils_src_prepare
}
src_configure() {
local mycmakeargs=(
-DBUILD_SHARED_LIBS=ON
- -DITK_USE_SYSTEM_DCMTK=ON
-DGDCM_USE_SYSTEM_OPENJPEG=ON
+ -DITK_FORBID_DOWNLOADS:BOOL=OFF
+ -DITK_USE_SYSTEM_DCMTK=ON
-DITK_USE_SYSTEM_DOUBLECONVERSION=ON
-DITK_USE_SYSTEM_CASTXML=ON
-DITK_USE_SYSTEM_HDF5=ON
@@ -86,7 +110,9 @@ src_configure() {
-DWRAP_ITK_JAVA=OFF
-DWRAP_ITK_TCL=OFF
-Ddouble-conversion_INCLUDE_DIRS="${EPREFIX}/usr/include/double-conversion"
- -DExternalData_OBJECT_STORES="${WORKDIR}/InsightToolkit-${MY_PV}/.ExternalData"
+ -DExternalData_OBJECT_STORES="${WORKDIR}/InsightToolkit-${PV}/.ExternalData"
+ -DModule_GenericLabelInterpolator:BOOL=ON
+ -DModule_ITKReview:BOOL=ON
-DBUILD_TESTING="$(usex test ON OFF)"
-DBUILD_EXAMPLES="$(usex examples ON OFF)"
-DITK_USE_REVIEW="$(usex review ON OFF)"
diff --git a/sci-libs/itk/metadata.xml b/sci-libs/itk/metadata.xml
index 8485fb7e1..7c4535324 100644
--- a/sci-libs/itk/metadata.xml
+++ b/sci-libs/itk/metadata.xml
@@ -14,7 +14,6 @@ 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>
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-libs/itk/, sci-libs/itk/files/
@ 2020-09-25 7:33 Horea Christian
0 siblings, 0 replies; 8+ messages in thread
From: Horea Christian @ 2020-09-25 7:33 UTC (permalink / raw
To: gentoo-commits
commit: 7112647657d76049ee42f5e2c86c05c2c1330760
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri Sep 25 07:33:20 2020 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Sep 25 07:33:20 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=71126476
sci-libs/itk: version bump 5.1.0
Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-libs/itk/files/itk-5.1.0-downloads.patch | 20 +++
sci-libs/itk/itk-5.1.0.ebuild | 188 +++++++++++++++++++++++++++
2 files changed, 208 insertions(+)
diff --git a/sci-libs/itk/files/itk-5.1.0-downloads.patch b/sci-libs/itk/files/itk-5.1.0-downloads.patch
new file mode 100644
index 000000000..34fdb76d1
--- /dev/null
+++ b/sci-libs/itk/files/itk-5.1.0-downloads.patch
@@ -0,0 +1,20 @@
+--- a/CMake/ITKDownloadSetup.cmake 2020-07-30 19:03:10.330325423 -0400
++++ b/CMake/ITKDownloadSetup.cmake 2020-07-30 19:03:10.330325423 -0400
+@@ -11,7 +11,7 @@
+
+ macro(itk_download_attempt_check _name)
+ if(ITK_FORBID_DOWNLOADS)
+- message(SEND_ERROR "Attempted to download ${_name} when ITK_FORBID_DOWNLOADS is ON")
++ message(WARNING "Attempted to download ${_name} when ITK_FORBID_DOWNLOADS is ON")
+ endif()
+ endmacro()
+
+--- a/Modules/Remote/GenericLabelInterpolator.remote.cmake 2020-04-25 14:30:53.000000000 -0400
++++ b/Modules/Remote/GenericLabelInterpolator.remote.cmake 2020-04-25 14:30:53.000000000 -0400
+@@ -44,6 +44,4 @@
+ itk_fetch_module(GenericLabelInterpolator
+ "A generic interpolator for multi-label images."
+ MODULE_COMPLIANCE_LEVEL 2
+- GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator.git
+- GIT_TAG b95fe46c7f4fe8002af67c67e6fe4e1f087bf6b7
+ )
diff --git a/sci-libs/itk/itk-5.1.0.ebuild b/sci-libs/itk/itk-5.1.0.ebuild
new file mode 100644
index 000000000..64fd555cb
--- /dev/null
+++ b/sci-libs/itk/itk-5.1.0.ebuild
@@ -0,0 +1,188 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python2_7 python3_{5,6,7} )
+
+inherit toolchain-funcs cmake python-single-r1
+
+MY_PN="InsightToolkit"
+MY_P="${MY_PN}-${PV}"
+GLI_HASH="a02cbeaf28cb3d28ac66b9ac651073530eb6ab78"
+TEST_HASH="0eb202e23ae81be123b1b26cf31a9ba743824700"
+declare -a GLI_TEST_HASHES=(
+ "a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a"
+ "bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f"
+)
+
+GLI_TEST_SRC=""
+for i in "${GLI_TEST_HASHES[@]}"; do
+ GLI_TEST_SRC+="https://data.kitware.com/api/v1/file/hashsum/sha512/${i} -> ${i} "
+done
+
+DESCRIPTION="NLM Insight Segmentation and Registration Toolkit"
+HOMEPAGE="http://www.itk.org"
+SRC_URI="
+ https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/${MY_P}.tar.gz
+ https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/archive/${GLI_HASH}.zip -> ITKGenericLabelInterpolator-${PV}.zip
+ test? (
+ https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/InsightData-${PV}.tar.gz
+ https://github.com/InsightSoftwareConsortium/ITKTestingData/archive/${TEST_HASH}.tar.gz
+ ${GLI_TEST_SRC}
+ )
+ "
+RESTRICT="primaryuri"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="debug doc examples fftw python review test vtkglue"
+# python will not work, this is a know issue upstream:
+# https://github.com/InsightSoftwareConsortium/ITK/issues/2005
+# https://github.com/InsightSoftwareConsortium/ITK/issues/1229
+# https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/issues/10
+
+RDEPEND="
+ dev-libs/double-conversion:0=
+ media-libs/openjpeg:2
+ media-libs/libpng:0=
+ media-libs/tiff:0=[jpeg]
+ sci-libs/dcmtk:0=
+ sci-libs/hdf5:0=[cxx]
+ sys-libs/zlib:0=
+ virtual/jpeg:0=
+ fftw? ( sci-libs/fftw:3.0= )
+ vtkglue? ( sci-libs/vtk:0=[rendering,python?] )
+"
+DEPEND="${RDEPEND}
+ sys-apps/coreutils
+ python? (
+ >=dev-lang/swig-2.0:0
+ dev-cpp/castxml
+ )
+ doc? ( app-doc/doxygen )
+"
+
+REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
+
+S="${WORKDIR}/${MY_P}"
+
+PATCHES=(
+ "${FILESDIR}"/tests.patch
+ "${FILESDIR}"/${P}-downloads.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 ${ITK_WRAP_DIMS} ]]; then
+ elog "For Python language bindings, you can define the dimensions"
+ elog "you want to create bindings for by setting"
+ elog " ITK_WRAP_DIMS=X;Y;Z..."
+ elog "in make.conf, default is 2;3 for 2D and 3D data"
+ fi
+}
+
+src_prepare() {
+ sed -i -e "s/find_package(OpenJPEG 2.0.0/find_package(OpenJPEG/g"\
+ Modules/ThirdParty/GDCM/src/gdcm/CMakeLists.txt
+ ln -sr ../ITKGenericLabelInterpolator-* Modules/External/ITKGenericLabelInterpolator || die
+ cmake_src_prepare
+ if use test; then
+ cp -rf "../ITKTestingData-${TEST_HASH}/"* ".ExternalData/" || die
+ mv "../ITKTestingData-${TEST_HASH}" "${BUILD_DIR}/.ExternalData" || die
+ for i in "${GLI_TEST_HASHES[@]}"; do
+ cp "${DISTDIR}/${i}" ".ExternalData/SHA512/" || die
+ cp "${DISTDIR}/${i}" "${BUILD_DIR}/.ExternalData/SHA512/" || die
+ done
+ fi
+}
+
+src_configure() {
+ local mycmakeargs=(
+ -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="$(usex review ON OFF)"
+ -DITK_USE_SYSTEM_DCMTK=ON
+ -DITK_USE_SYSTEM_DOUBLECONVERSION=ON
+ -DITK_USE_SYSTEM_CASTXML=ON
+ -DITK_USE_SYSTEM_HDF5=ON
+ -DITK_USE_SYSTEM_JPEG=ON
+ -DITK_USE_SYSTEM_PNG=ON
+ -DITK_USE_SYSTEM_SWIG=ON
+ -DITK_USE_SYSTEM_TIFF=ON
+ -DITK_USE_SYSTEM_ZLIB=ON
+ -DITK_USE_KWSTYLE=OFF
+ -DITK_BUILD_DEFAULT_MODULES=ON
+ -DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}"
+ -DModule_GenericLabelInterpolator:BOOL=ON
+ -DModule_ITKReview:BOOL=ON
+ -DWRAP_ITK_JAVA=OFF
+ -DWRAP_ITK_TCL=OFF
+ )
+ 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="${ITK_WRAP_DIMS:-2;3}"
+ )
+ else
+ mycmakeargs+=(
+ -DITK_WRAP_PYTHON=OFF
+ )
+ fi
+ cmake_src_configure
+}
+
+src_install() {
+ cmake_src_install
+
+ if use examples; then
+ insinto /usr/share/doc/${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
+}
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-libs/itk/, sci-libs/itk/files/
@ 2022-08-23 10:58 Andrew Ammerlaan
0 siblings, 0 replies; 8+ messages in thread
From: Andrew Ammerlaan @ 2022-08-23 10:58 UTC (permalink / raw
To: gentoo-commits
commit: b4acbb5f52ed06ad45b5a4e877498a6c9f683d4e
Author: François-Xavier Carton <fx.carton91 <AT> gmail <DOT> com>
AuthorDate: Fri Jun 10 13:16:57 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Aug 23 10:58:09 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b4acbb5f
sci-libs/itk: bump to 5.2.1
Signed-off-by: François-Xavier Carton <fx.carton91 <AT> gmail.com>
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
Closes: https://github.com/gentoo/sci/pull/1154
.../itk-5.2.1-fix-castxml-clang-attr-malloc.patch | 25 +
sci-libs/itk/files/itk-5.2.1-system-openjpeg.patch | 558 +++++++++++++++++++++
.../itk/files/itk-5.2.1-system-tiff-has-64.patch | 18 +
sci-libs/itk/files/itk-5.2.1-upstream-fixes.patch | 255 ++++++++++
sci-libs/itk/itk-5.2.1.ebuild | 246 +++++++++
5 files changed, 1102 insertions(+)
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..2e547d9ca
--- /dev/null
+++ b/sci-libs/itk/files/itk-5.2.1-upstream-fixes.patch
@@ -0,0 +1,255 @@
+https://github.com/InsightSoftwareConsortium/ITK/commit/2a7f5ed199926999b67f61a97c2c9a2595a11558.patch
+https://github.com/InsightSoftwareConsortium/ITK/commit/0c31aa688e82a34e5430873bc6176740fd09ad75.patch
+https://github.com/InsightSoftwareConsortium/ITK/commit/28325d921a9b8793e6aaefd612f53989f951d19c.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}" "${CMAKE_CURRENT_BINARY_DIR}/detect_site_package_path.py"
+ OUTPUT_VARIABLE py_spp
diff --git a/sci-libs/itk/itk-5.2.1.ebuild b/sci-libs/itk/itk-5.2.1.ebuild
new file mode 100644
index 000000000..25292269f
--- /dev/null
+++ b/sci-libs/itk/itk-5.2.1.ebuild
@@ -0,0 +1,246 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{9..10} )
+VIRTUALX_REQUIRED="manual"
+
+inherit cmake python-single-r1 virtualx
+
+MY_PN="InsightToolkit"
+MY_P="${MY_PN}-${PV}"
+GLI_HASH="89da9305f5750d3990ca9fd35ecc5ce0b39c71a6"
+TEST_HASH="7ab9d41ad5b42ccbe8adcaf0b24416d439a264d0"
+declare -a GLI_TEST_HASHES=(
+ "a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a"
+ "bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f"
+)
+
+GLI_TEST_SRC=""
+for i in "${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
+ 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-doc/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
+
+ 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="${ITK_COMPUTER_MEMORY_SIZE:-1}"
+ -DModule_GenericLabelInterpolator:BOOL=ON
+ -DModule_ITKReview:BOOL=ON
+ -DWRAP_ITK_JAVA=OFF
+ -DWRAP_ITK_TCL=OFF
+ -DITKV4_COMPATIBILITY:BOOL=$(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
+}
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-libs/itk/, sci-libs/itk/files/
@ 2022-08-31 10:30 Andrew Ammerlaan
0 siblings, 0 replies; 8+ messages in thread
From: Andrew Ammerlaan @ 2022-08-31 10:30 UTC (permalink / raw
To: gentoo-commits
commit: e183cbc1d2404c5ce6348627365cdc1aa483c375
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Wed Aug 31 10:30:15 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Wed Aug 31 10:30:15 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e183cbc1
sci-libs/itk: drop 5.0.1, 5.1.0
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
...p-TransformFileReader-TransformFileWriter.patch | 50 ------
...itkQuasiNewtonOptimizerv4-wrapping-warnin.patch | 28 ---
...itkGradientDescentOptimizerv4-wrapping-wa.patch | 73 --------
...OptimizerParameterScalesEstimatorTemplate.patch | 30 ----
.../0005-make-gdcm-helper-library-static.patch | 11 --
sci-libs/itk/files/ITKModuleRemote.patch | 45 -----
sci-libs/itk/files/itk-5.1.0-downloads.patch | 20 ---
sci-libs/itk/files/itk-5.1.0-include_limits.patch | 10 --
sci-libs/itk/files/nrrdio-linking.patch | 15 --
sci-libs/itk/files/tests.patch | 41 -----
sci-libs/itk/itk-5.0.1.ebuild | 178 -------------------
sci-libs/itk/itk-5.1.0.ebuild | 191 ---------------------
12 files changed, 692 deletions(-)
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_${t}}")
-+ endforeach(t)
-+itk_end_wrap_class()
-
diff --git a/sci-libs/itk/files/0005-make-gdcm-helper-library-static.patch b/sci-libs/itk/files/0005-make-gdcm-helper-library-static.patch
deleted file mode 100644
index d760ac7ba..000000000
--- a/sci-libs/itk/files/0005-make-gdcm-helper-library-static.patch
+++ /dev/null
@@ -1,11 +0,0 @@
-diff --git a/Modules/ThirdParty/GDCM/src/CMakeLists.txt b/Modules/ThirdParty/GDCM/src/CMakeLists.txt
-index e98077c..70f4286 100644
---- a/Modules/ThirdParty/GDCM/src/CMakeLists.txt
-+++ b/Modules/ThirdParty/GDCM/src/CMakeLists.txt
-@@ -1,5 +1,5 @@
- if(ITK_USE_SYSTEM_GDCM)
-- add_library(ITKGDCM ITK-GDCM.cxx)
-+ add_library(ITKGDCM STATIC ITK-GDCM.cxx)
- target_link_libraries(ITKGDCM gdcmDICT gdcmMSFF)
- itk_module_target(ITKGDCM)
- return()
diff --git a/sci-libs/itk/files/ITKModuleRemote.patch b/sci-libs/itk/files/ITKModuleRemote.patch
deleted file mode 100644
index eb130159a..000000000
--- a/sci-libs/itk/files/ITKModuleRemote.patch
+++ /dev/null
@@ -1,45 +0,0 @@
-Disable automatic git clone attempt for modules:
-https://github.com/InsightSoftwareConsortium/ITK/issues/1157
-
---- a/CMake/ITKModuleRemote.cmake 2019-08-13 18:10:33.385472767 +0200
-+++ b/CMake/ITKModuleRemote.cmake 2019-08-13 18:12:04.020198966 +0200
-@@ -165,39 +165,4 @@
- set(Module_${_name} ON CACHE FORCE "${_description}")
- endif()
-
-- if(Module_${_name})
-- itk_download_attempt_check(Module_${_name})
-- include(CMakeParseArguments)
-- cmake_parse_arguments(_fetch_options "" "GIT_REPOSITORY;GIT_TAG" "" ${ARGN})
-- find_package(Git)
-- if(NOT GIT_EXECUTABLE)
-- message(FATAL_ERROR "error: could not find git for clone of ${_name}")
-- endif()
-- execute_process(
-- COMMAND "${GIT_EXECUTABLE}" --version
-- OUTPUT_VARIABLE ov
-- OUTPUT_STRIP_TRAILING_WHITESPACE
-- )
-- string(REGEX REPLACE "^git version (.+)$" "\\1" _version "${ov}")
-- if("${_version}" VERSION_LESS 1.6.6)
-- message(FATAL_ERROR "Git version 1.6.6 or later is required.")
-- endif()
--
-- set(REMOTE_GIT_TAG "${_fetch_options_GIT_TAG}")
--
-- if( DEFINED REMOTE_GIT_TAG_${_name} AND NOT "${REMOTE_GIT_TAG_${_name}}" STREQUAL "${_fetch_options_GIT_TAG}")
-- set(REMOTE_GIT_TAG "${REMOTE_GIT_TAG_${_name}}")
-- message(STATUS "NOTE: Using override 'REMOTE_GIT_TAG_${_name}=${REMOTE_GIT_TAG}'\n"
-- " instead of value 'GIT_TAG=${_fetch_options_GIT_TAG}'\n"
-- " specified in file ${ITK_SOURCE_DIR}/Modules/Remote/${_name}.remote.cmake'")
-- endif()
-- set(REMOTE_GIT_TAG_${_name} "${REMOTE_GIT_TAG}" CACHE STRING "Override default GIT_TAG value for remote module ${_name}")
-- mark_as_advanced(REMOTE_GIT_TAG_${_name})
--
-- _fetch_with_git("${GIT_EXECUTABLE}"
-- "${_fetch_options_GIT_REPOSITORY}"
-- "${REMOTE_GIT_TAG}"
-- "${ITK_SOURCE_DIR}/Modules/Remote/${_name}"
-- )
-- endif()
- endfunction()
diff --git a/sci-libs/itk/files/itk-5.1.0-downloads.patch b/sci-libs/itk/files/itk-5.1.0-downloads.patch
deleted file mode 100644
index 34fdb76d1..000000000
--- a/sci-libs/itk/files/itk-5.1.0-downloads.patch
+++ /dev/null
@@ -1,20 +0,0 @@
---- a/CMake/ITKDownloadSetup.cmake 2020-07-30 19:03:10.330325423 -0400
-+++ b/CMake/ITKDownloadSetup.cmake 2020-07-30 19:03:10.330325423 -0400
-@@ -11,7 +11,7 @@
-
- macro(itk_download_attempt_check _name)
- if(ITK_FORBID_DOWNLOADS)
-- message(SEND_ERROR "Attempted to download ${_name} when ITK_FORBID_DOWNLOADS is ON")
-+ message(WARNING "Attempted to download ${_name} when ITK_FORBID_DOWNLOADS is ON")
- endif()
- endmacro()
-
---- a/Modules/Remote/GenericLabelInterpolator.remote.cmake 2020-04-25 14:30:53.000000000 -0400
-+++ b/Modules/Remote/GenericLabelInterpolator.remote.cmake 2020-04-25 14:30:53.000000000 -0400
-@@ -44,6 +44,4 @@
- itk_fetch_module(GenericLabelInterpolator
- "A generic interpolator for multi-label images."
- MODULE_COMPLIANCE_LEVEL 2
-- GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator.git
-- GIT_TAG b95fe46c7f4fe8002af67c67e6fe4e1f087bf6b7
- )
diff --git a/sci-libs/itk/files/itk-5.1.0-include_limits.patch b/sci-libs/itk/files/itk-5.1.0-include_limits.patch
deleted file mode 100644
index 9a8fae820..000000000
--- a/sci-libs/itk/files/itk-5.1.0-include_limits.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- a/Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmImageChangePhotometricInterpretation.h
-+++ a/Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmImageChangePhotometricInterpretation.h
-@@ -16,6 +16,7 @@
-
- #include "gdcmImageToImageFilter.h"
- #include "gdcmPhotometricInterpretation.h"
-+#include <limits>
-
- namespace gdcm
- {
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 ${ITK_LIBRARY_PROPERTIES})
diff --git a/sci-libs/itk/files/tests.patch b/sci-libs/itk/files/tests.patch
deleted file mode 100644
index c24714e4d..000000000
--- a/sci-libs/itk/files/tests.patch
+++ /dev/null
@@ -1,41 +0,0 @@
-Known to fail by upstream:
-https://github.com/InsightSoftwareConsortium/ITK/issues/1212#issuecomment-527998115
-
---- a/Modules/Bridge/VtkGlue/test/CMakeLists.txt 2019-09-09 00:45:14.736032139 +0200
-+++ b/Modules/Bridge/VtkGlue/test/CMakeLists.txt 2019-09-09 00:49:42.183935497 +0200
-@@ -7,8 +7,6 @@
- if(NOT VTK_RENDERING_BACKEND STREQUAL "None")
- list(APPEND ITKVtkGlueTests
- itkVtkMedianFilterTest.cxx
-- itkVtkConnectedComponentImageFilterTest.cxx
-- QuickViewTest.cxx
- # ### runViewImage ###
- # No test generated. Use it for view images (2D or 3D) with:
- # ITKVtkGlueTestDriver runViewImage image_file
-@@ -40,26 +38,3 @@
- NAME itkVTKImageToImageFilterTest
- COMMAND ITKVtkGlueTestDriver
- itkVTKImageToImageFilterTest)
--
--if(NOT VTK_RENDERING_BACKEND STREQUAL "None")
-- itk_add_test(
-- NAME itkVtkMedianImageFilterTest
-- COMMAND ITKVtkGlueTestDriver
-- itkVtkMedianFilterTest DATA{${ITK_DATA_ROOT}/Input/cthead1.png} 2)
-- set_property(TEST itkVtkMedianImageFilterTest APPEND PROPERTY LABELS REQUIRES_DISPLAY)
--
-- itk_add_test(
-- NAME QuickViewTest
-- COMMAND ITKVtkGlueTestDriver
-- --compare DATA{Baseline/QuickViewTest.png,:}
-- ${ITK_TEST_OUTPUT_DIR}/QuickViewTest0.png
-- --compareNumberOfPixelsTolerance 1500
-- QuickViewTest DATA{${ITK_DATA_ROOT}/Input/peppers.png} ${ITK_TEST_OUTPUT_DIR})
-- set_property(TEST QuickViewTest APPEND PROPERTY LABELS REQUIRES_DISPLAY)
--
-- itk_add_test(
-- NAME itkVtkConnectedComponentImageFilterTest
-- COMMAND ITKVtkGlueTestDriver
-- itkVtkConnectedComponentImageFilterTest DATA{${ITK_DATA_ROOT}/Input/cthead1.png})
-- set_property(TEST itkVtkConnectedComponentImageFilterTest APPEND PROPERTY LABELS REQUIRES_DISPLAY)
--endif()
diff --git a/sci-libs/itk/itk-5.0.1.ebuild b/sci-libs/itk/itk-5.0.1.ebuild
deleted file mode 100644
index 4580c659a..000000000
--- a/sci-libs/itk/itk-5.0.1.ebuild
+++ /dev/null
@@ -1,178 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{8..10} )
-
-inherit cmake python-single-r1
-
-MY_PN="InsightToolkit"
-MY_P="${MY_PN}-${PV}"
-GLI_HASH="187ab99b7d42718c99e5017f0acd3900d7469bd1"
-GLI_TEST_HASH="57b5d5de8d777f10f269445a"
-
-DESCRIPTION="NLM Insight Segmentation and Registration Toolkit"
-HOMEPAGE="http://www.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
- test? (
- https://data.kitware.com/api/v1/folder/${GLI_TEST_HASH}/download -> ITKGenericLabelInterpolator_test-${PV}.zip
- https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/InsightData-${PV}.tar.gz
- )
- "
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="debug doc examples fftw python review test vtkglue"
-RESTRICT="!test? ( test )"
-# python will not work, this is a know issue upstream:
-# https://github.com/InsightSoftwareConsortium/ITK/issues/1229
-# https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/issues/10
-
-RDEPEND="
- dev-libs/double-conversion:0=
- media-libs/openjpeg:2
- media-libs/libpng:0=
- media-libs/tiff:0=
- sci-libs/dcmtk:0=
- sci-libs/hdf5:0=[cxx]
- sys-libs/zlib:0=
- media-libs/libjpeg-turbo:0=
- fftw? ( sci-libs/fftw:3.0= )
- vtkglue? ( sci-libs/vtk:0=[rendering,python?] )
- python? ( ${PYTHON_DEPS} )
-"
-DEPEND="${RDEPEND}
- sys-apps/coreutils
- python? (
- >=dev-lang/swig-2.0:0
- dev-cpp/castxml
- )
- doc? ( app-doc/doxygen )
-"
-BDEPEND="app-arch/unzip"
-
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-S="${WORKDIR}/${MY_P}"
-
-PATCHES=(
- "${FILESDIR}"/ITKModuleRemote.patch
- "${FILESDIR}"/tests.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 ${ITK_WRAP_DIMS} ]]; then
- elog "For Python language bindings, you can define the dimensions"
- elog "you want to create bindings for by setting"
- elog " ITK_WRAP_DIMS=X;Y;Z..."
- elog "in make.conf, default is 2;3 for 2D and 3D data"
- fi
-}
-
-src_prepare() {
- sed -i -e "s/find_package(OpenJPEG 2.0.0/find_package(OpenJPEG/g"\
- Modules/ThirdParty/GDCM/src/gdcm/CMakeLists.txt
- ln -sr ../ITKGenericLabelInterpolator-* Modules/Remote/ITKGenericLabelInterpolator || die
- if use test; then
- for filename in ../GenericLabelInterpolator/test/*/*mha; do
- MD5=$(md5sum $filename) || die
- MD5=${MD5% *} || die
- cp "$filename" ".ExternalData/MD5/${MD5}" || die
- done
- fi
- cmake_src_prepare
-}
-
-src_configure() {
- local mycmakeargs=(
- -DBUILD_SHARED_LIBS=ON
- -DGDCM_USE_SYSTEM_OPENJPEG=ON
- -DITK_FORBID_DOWNLOADS:BOOL=OFF
- -DITK_USE_SYSTEM_DCMTK=ON
- -DITK_USE_SYSTEM_DOUBLECONVERSION=ON
- -DITK_USE_SYSTEM_CASTXML=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_USE_KWSTYLE=OFF
- -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"
- -DExternalData_OBJECT_STORES="${WORKDIR}/InsightToolkit-${PV}/.ExternalData"
- -DModule_GenericLabelInterpolator:BOOL=ON
- -DModule_ITKReview:BOOL=ON
- -DBUILD_TESTING="$(usex test ON OFF)"
- -DBUILD_EXAMPLES="$(usex examples ON OFF)"
- -DITK_USE_REVIEW="$(usex review ON OFF)"
- -DITK_BUILD_DOCUMENTATION="$(usex doc ON OFF)"
- -DITK_INSTALL_LIBRARY_DIR=$(get_libdir)
- )
- if use fftw; then
- mycmakeargs+=(
- -DUSE_FFTWD=ON
- -DUSE_FFTWF=ON
- -DUSE_SYSTEM_FFTW=ON
- -DITK_WRAP_double=ON
- -DITK_WRAP_vector_double=ON
- -DITK_WRAP_covariant_vector_double=ON
- -DITK_WRAP_complex_double=ON
- )
- fi
- if use vtkglue; then
- mycmakeargs+=(
- -DModule_ITKVtkGlue=ON
- )
- fi
- if use python; then
- mycmakeargs+=(
- -DITK_WRAP_PYTHON=ON
- -DITK_WRAP_DIMS="${ITK_WRAP_DIMS:-2;3}"
- )
- else
- mycmakeargs+=(
- -DITK_WRAP_PYTHON=OFF
- )
- fi
- cmake_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}
- local ldpath="${EPREFIX}/usr/$(get_libdir)/InsightToolkit"
- if use python; then
- echo "PYTHONPATH=${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> "${T}"/40${PN}
- ldpath="${ldpath}:${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib"
- fi
- echo "LDPATH=${ldpath}" >> "${T}"/40${PN}
- doenvd "${T}"/40${PN}
-
- if use doc; then
- cd "${WORKDIR}"/html || die
- rm *.md5 || die "Failed to remove superfluous hashes"
- einfo "Installing API docs. This may take some time."
- docinto api-docs
- dodoc -r *
- fi
-}
diff --git a/sci-libs/itk/itk-5.1.0.ebuild b/sci-libs/itk/itk-5.1.0.ebuild
deleted file mode 100644
index e6e0b25f9..000000000
--- a/sci-libs/itk/itk-5.1.0.ebuild
+++ /dev/null
@@ -1,191 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{8..10} )
-
-inherit cmake python-single-r1
-
-MY_PN="InsightToolkit"
-MY_P="${MY_PN}-${PV}"
-GLI_HASH="a02cbeaf28cb3d28ac66b9ac651073530eb6ab78"
-TEST_HASH="0eb202e23ae81be123b1b26cf31a9ba743824700"
-declare -a GLI_TEST_HASHES=(
- "a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a"
- "bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f"
-)
-
-GLI_TEST_SRC=""
-for i in "${GLI_TEST_HASHES[@]}"; do
- GLI_TEST_SRC+="https://data.kitware.com/api/v1/file/hashsum/sha512/${i} -> ${P}-test-${i} "
-done
-
-DESCRIPTION="NLM Insight Segmentation and Registration Toolkit"
-HOMEPAGE="http://www.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
- 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"
-RESTRICT="!test? ( test )"
-# python will not work, this is a know issue upstream:
-# https://github.com/InsightSoftwareConsortium/ITK/issues/2005
-# https://github.com/InsightSoftwareConsortium/ITK/issues/1229
-# https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/issues/10
-
-RDEPEND="
- dev-libs/double-conversion:0=
- media-libs/openjpeg:2
- media-libs/libpng:0=
- media-libs/tiff:0=[jpeg]
- sci-libs/dcmtk:0=
- sci-libs/hdf5:0=[cxx]
- sys-libs/zlib:0=
- media-libs/libjpeg-turbo:0=
- fftw? ( sci-libs/fftw:3.0= )
- vtkglue? ( sci-libs/vtk:0=[rendering,python?] )
- python? ( ${PYTHON_DEPS} )
-"
-DEPEND="${RDEPEND}
- sys-apps/coreutils
- python? (
- >=dev-lang/swig-2.0:0
- dev-cpp/castxml
- )
- doc? ( app-doc/doxygen )
-"
-
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-S="${WORKDIR}/${MY_P}"
-
-PATCHES=(
- "${FILESDIR}"/tests.patch
- "${FILESDIR}"/${P}-downloads.patch
- "${FILESDIR}"/${P}-include_limits.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 ${ITK_WRAP_DIMS} ]]; then
- elog "For Python language bindings, you can define the dimensions"
- elog "you want to create bindings for by setting"
- elog " ITK_WRAP_DIMS=X;Y;Z..."
- elog "in make.conf, default is 2;3 for 2D and 3D data"
- fi
-}
-
-src_prepare() {
- sed -i -e "s/find_package(OpenJPEG 2.0.0/find_package(OpenJPEG/g"\
- Modules/ThirdParty/GDCM/src/gdcm/CMakeLists.txt
- ln -sr ../ITKGenericLabelInterpolator-* Modules/External/ITKGenericLabelInterpolator || die
- cmake_src_prepare
- if use test; then
- cp -rf "../ITKTestingData-${TEST_HASH}/"* ".ExternalData/" || die
- mv "../ITKTestingData-${TEST_HASH}" "${BUILD_DIR}/.ExternalData" || die
- for i in "${GLI_TEST_HASHES[@]}"; do
- cp "${DISTDIR}/${i}" ".ExternalData/SHA512/" || die
- cp "${DISTDIR}/${i}" "${BUILD_DIR}/.ExternalData/SHA512/" || die
- done
- fi
-}
-
-src_configure() {
- local mycmakeargs=(
- -DITK_BUILD_DOCUMENTATION="$(usex doc ON OFF)"
- -DBUILD_EXAMPLES="$(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_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_USE_KWSTYLE=OFF
- -DITK_BUILD_DEFAULT_MODULES=ON
- -DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}"
- -DModule_GenericLabelInterpolator:BOOL=ON
- -DModule_ITKReview:BOOL=ON
- -DWRAP_ITK_JAVA=OFF
- -DWRAP_ITK_TCL=OFF
- -DITKV4_COMPATIBILITY:BOOL=$(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
- -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}
- local ldpath="${EPREFIX}/usr/$(get_libdir)/InsightToolkit"
- if use python; then
- echo "PYTHONPATH=${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> "${T}"/40${PN}
- ldpath="${ldpath}:${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib"
- fi
- echo "LDPATH=${ldpath}" >> "${T}"/40${PN}
- 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
-}
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-libs/itk/, sci-libs/itk/files/
@ 2022-09-15 11:17 Andrew Ammerlaan
0 siblings, 0 replies; 8+ messages in thread
From: Andrew Ammerlaan @ 2022-09-15 11:17 UTC (permalink / raw
To: gentoo-commits
commit: 9ff3b1053e275f3a30fa574c79f3ee1af8cbeca0
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Thu Sep 15 11:09:45 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Thu Sep 15 11:09:45 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=9ff3b105
Revert "sci-libs/itk: add 5.1.0"
This reverts commit 42b8aadc9ce1de416e55dba98c3ba02a0177366f.
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-libs/itk/files/itk-5.1.0-downloads.patch | 20 ---
sci-libs/itk/files/itk-5.1.0-include_limits.patch | 10 --
sci-libs/itk/files/tests.patch | 41 -----
sci-libs/itk/itk-5.1.0.ebuild | 191 ----------------------
4 files changed, 262 deletions(-)
diff --git a/sci-libs/itk/files/itk-5.1.0-downloads.patch b/sci-libs/itk/files/itk-5.1.0-downloads.patch
deleted file mode 100644
index 34fdb76d1..000000000
--- a/sci-libs/itk/files/itk-5.1.0-downloads.patch
+++ /dev/null
@@ -1,20 +0,0 @@
---- a/CMake/ITKDownloadSetup.cmake 2020-07-30 19:03:10.330325423 -0400
-+++ b/CMake/ITKDownloadSetup.cmake 2020-07-30 19:03:10.330325423 -0400
-@@ -11,7 +11,7 @@
-
- macro(itk_download_attempt_check _name)
- if(ITK_FORBID_DOWNLOADS)
-- message(SEND_ERROR "Attempted to download ${_name} when ITK_FORBID_DOWNLOADS is ON")
-+ message(WARNING "Attempted to download ${_name} when ITK_FORBID_DOWNLOADS is ON")
- endif()
- endmacro()
-
---- a/Modules/Remote/GenericLabelInterpolator.remote.cmake 2020-04-25 14:30:53.000000000 -0400
-+++ b/Modules/Remote/GenericLabelInterpolator.remote.cmake 2020-04-25 14:30:53.000000000 -0400
-@@ -44,6 +44,4 @@
- itk_fetch_module(GenericLabelInterpolator
- "A generic interpolator for multi-label images."
- MODULE_COMPLIANCE_LEVEL 2
-- GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator.git
-- GIT_TAG b95fe46c7f4fe8002af67c67e6fe4e1f087bf6b7
- )
diff --git a/sci-libs/itk/files/itk-5.1.0-include_limits.patch b/sci-libs/itk/files/itk-5.1.0-include_limits.patch
deleted file mode 100644
index 9a8fae820..000000000
--- a/sci-libs/itk/files/itk-5.1.0-include_limits.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- a/Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmImageChangePhotometricInterpretation.h
-+++ a/Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmImageChangePhotometricInterpretation.h
-@@ -16,6 +16,7 @@
-
- #include "gdcmImageToImageFilter.h"
- #include "gdcmPhotometricInterpretation.h"
-+#include <limits>
-
- namespace gdcm
- {
diff --git a/sci-libs/itk/files/tests.patch b/sci-libs/itk/files/tests.patch
deleted file mode 100644
index c24714e4d..000000000
--- a/sci-libs/itk/files/tests.patch
+++ /dev/null
@@ -1,41 +0,0 @@
-Known to fail by upstream:
-https://github.com/InsightSoftwareConsortium/ITK/issues/1212#issuecomment-527998115
-
---- a/Modules/Bridge/VtkGlue/test/CMakeLists.txt 2019-09-09 00:45:14.736032139 +0200
-+++ b/Modules/Bridge/VtkGlue/test/CMakeLists.txt 2019-09-09 00:49:42.183935497 +0200
-@@ -7,8 +7,6 @@
- if(NOT VTK_RENDERING_BACKEND STREQUAL "None")
- list(APPEND ITKVtkGlueTests
- itkVtkMedianFilterTest.cxx
-- itkVtkConnectedComponentImageFilterTest.cxx
-- QuickViewTest.cxx
- # ### runViewImage ###
- # No test generated. Use it for view images (2D or 3D) with:
- # ITKVtkGlueTestDriver runViewImage image_file
-@@ -40,26 +38,3 @@
- NAME itkVTKImageToImageFilterTest
- COMMAND ITKVtkGlueTestDriver
- itkVTKImageToImageFilterTest)
--
--if(NOT VTK_RENDERING_BACKEND STREQUAL "None")
-- itk_add_test(
-- NAME itkVtkMedianImageFilterTest
-- COMMAND ITKVtkGlueTestDriver
-- itkVtkMedianFilterTest DATA{${ITK_DATA_ROOT}/Input/cthead1.png} 2)
-- set_property(TEST itkVtkMedianImageFilterTest APPEND PROPERTY LABELS REQUIRES_DISPLAY)
--
-- itk_add_test(
-- NAME QuickViewTest
-- COMMAND ITKVtkGlueTestDriver
-- --compare DATA{Baseline/QuickViewTest.png,:}
-- ${ITK_TEST_OUTPUT_DIR}/QuickViewTest0.png
-- --compareNumberOfPixelsTolerance 1500
-- QuickViewTest DATA{${ITK_DATA_ROOT}/Input/peppers.png} ${ITK_TEST_OUTPUT_DIR})
-- set_property(TEST QuickViewTest APPEND PROPERTY LABELS REQUIRES_DISPLAY)
--
-- itk_add_test(
-- NAME itkVtkConnectedComponentImageFilterTest
-- COMMAND ITKVtkGlueTestDriver
-- itkVtkConnectedComponentImageFilterTest DATA{${ITK_DATA_ROOT}/Input/cthead1.png})
-- set_property(TEST itkVtkConnectedComponentImageFilterTest APPEND PROPERTY LABELS REQUIRES_DISPLAY)
--endif()
diff --git a/sci-libs/itk/itk-5.1.0.ebuild b/sci-libs/itk/itk-5.1.0.ebuild
deleted file mode 100644
index 34d2c215d..000000000
--- a/sci-libs/itk/itk-5.1.0.ebuild
+++ /dev/null
@@ -1,191 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{8..10} )
-
-inherit cmake python-single-r1
-
-MY_PN="InsightToolkit"
-MY_P="${MY_PN}-${PV}"
-GLI_HASH="a02cbeaf28cb3d28ac66b9ac651073530eb6ab78"
-TEST_HASH="0eb202e23ae81be123b1b26cf31a9ba743824700"
-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} -> ${P}-test-${i} "
-done
-
-DESCRIPTION="NLM Insight Segmentation and Registration Toolkit"
-HOMEPAGE="http://www.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
- 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"
-RESTRICT="!test? ( test )"
-# python will not work, this is a know issue upstream:
-# https://github.com/InsightSoftwareConsortium/ITK/issues/2005
-# https://github.com/InsightSoftwareConsortium/ITK/issues/1229
-# https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/issues/10
-
-RDEPEND="
- dev-libs/double-conversion:0=
- media-libs/openjpeg:2
- media-libs/libpng:0=
- media-libs/tiff:0=[jpeg]
- sci-libs/dcmtk:0=
- sci-libs/hdf5:0=[cxx]
- sys-libs/zlib:0=
- media-libs/libjpeg-turbo:0=
- fftw? ( sci-libs/fftw:3.0= )
- vtkglue? ( sci-libs/vtk:0=[rendering,python?] )
- python? ( ${PYTHON_DEPS} )
-"
-DEPEND="${RDEPEND}
- sys-apps/coreutils
- python? (
- >=dev-lang/swig-2.0:0
- dev-libs/castxml
- )
- doc? ( app-doc/doxygen )
-"
-
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-S="${WORKDIR}/${MY_P}"
-
-PATCHES=(
- "${FILESDIR}"/tests.patch
- "${FILESDIR}"/${P}-downloads.patch
- "${FILESDIR}"/${P}-include_limits.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 ${ITK_WRAP_DIMS} ]]; then
- elog "For Python language bindings, you can define the dimensions"
- elog "you want to create bindings for by setting"
- elog " ITK_WRAP_DIMS=X;Y;Z..."
- elog "in make.conf, default is 2;3 for 2D and 3D data"
- fi
-}
-
-src_prepare() {
- sed -i -e "s/find_package(OpenJPEG 2.0.0/find_package(OpenJPEG/g"\
- Modules/ThirdParty/GDCM/src/gdcm/CMakeLists.txt
- ln -sr ../ITKGenericLabelInterpolator-* Modules/External/ITKGenericLabelInterpolator || die
- cmake_src_prepare
- if use test; then
- cp -rf "../ITKTestingData-${TEST_HASH}/"* ".ExternalData/" || die
- mv "../ITKTestingData-${TEST_HASH}" "${BUILD_DIR}/.ExternalData" || die
- for i in "${GLI_TEST_HASHES[@]}"; do
- cp "${DISTDIR}/${i}" ".ExternalData/SHA512/" || die
- cp "${DISTDIR}/${i}" "${BUILD_DIR}/.ExternalData/SHA512/" || die
- done
- fi
-}
-
-src_configure() {
- local mycmakeargs=(
- -DITK_BUILD_DOCUMENTATION="$(usex doc ON OFF)"
- -DBUILD_EXAMPLES="$(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_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_USE_KWSTYLE=OFF
- -DITK_BUILD_DEFAULT_MODULES=ON
- -DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}"
- -DModule_GenericLabelInterpolator:BOOL=ON
- -DModule_ITKReview:BOOL=ON
- -DWRAP_ITK_JAVA=OFF
- -DWRAP_ITK_TCL=OFF
- -DITKV4_COMPATIBILITY:BOOL=$(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
- -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}
- local ldpath="${EPREFIX}/usr/$(get_libdir)/InsightToolkit"
- if use python; then
- echo "PYTHONPATH=${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> "${T}"/40${PN}
- ldpath="${ldpath}:${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib"
- fi
- echo "LDPATH=${ldpath}" >> "${T}"/40${PN}
- 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
-}
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-libs/itk/, sci-libs/itk/files/
@ 2022-09-30 10:18 Andrew Ammerlaan
0 siblings, 0 replies; 8+ messages in thread
From: Andrew Ammerlaan @ 2022-09-30 10:18 UTC (permalink / raw
To: gentoo-commits
commit: 76b20521901742c59aa823035357a3a49ebb0aad
Author: François-Xavier Carton <fx.carton91 <AT> gmail <DOT> com>
AuthorDate: Thu Sep 29 18:08:30 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Fri Sep 30 06:49:55 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=76b20521
sci-libs/itk: add upstream patch to fix building tests
Needed since commit b6218b "sci-libs/itk: add AdaptiveDenoising module"
because the commit used for that remote module is too recent and needs
that ITK commit.
Signed-off-by: François-Xavier Carton <fx.carton91 <AT> gmail.com>
Closes: https://github.com/gentoo/sci/pull/1172
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-libs/itk/files/itk-5.2.1-upstream-fixes.patch | 54 ++++++++++++++++++++++
.../{itk-5.2.1-r1.ebuild => itk-5.2.1-r2.ebuild} | 0
2 files changed, 54 insertions(+)
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
index 2e547d9ca..2af8c4998 100644
--- a/sci-libs/itk/files/itk-5.2.1-upstream-fixes.patch
+++ b/sci-libs/itk/files/itk-5.2.1-upstream-fixes.patch
@@ -1,6 +1,7 @@
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>
@@ -253,3 +254,56 @@ index fca3d999b87..3b7a1d37334 100644
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/itk-5.2.1-r1.ebuild b/sci-libs/itk/itk-5.2.1-r2.ebuild
similarity index 100%
rename from sci-libs/itk/itk-5.2.1-r1.ebuild
rename to sci-libs/itk/itk-5.2.1-r2.ebuild
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-libs/itk/, sci-libs/itk/files/
@ 2023-03-25 1:49 Horea Christian
0 siblings, 0 replies; 8+ messages in thread
From: Horea Christian @ 2023-03-25 1:49 UTC (permalink / raw
To: gentoo-commits
commit: d23b080b9afe74c6590a9827d505e9234c00deb0
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sat Mar 25 01:48:55 2023 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sat Mar 25 01:48:55 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=d23b080b
sci-libs/itk: add 5.3.0
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-libs/itk/files/itk-5.3.0-system-openjpeg.patch | 550 +++++++++++++++++++++
sci-libs/itk/itk-5.3.0.ebuild | 251 ++++++++++
2 files changed, 801 insertions(+)
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} ${ITKOpenJPEG_LIBRARIES})
+ itk_module_target(ITKReview)
+
+
diff --git a/sci-libs/itk/itk-5.3.0.ebuild b/sci-libs/itk/itk-5.3.0.ebuild
new file mode 100644
index 000000000..54b7c89b3
--- /dev/null
+++ b/sci-libs/itk/itk-5.3.0.ebuild
@@ -0,0 +1,251 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+VIRTUALX_REQUIRED="manual"
+
+inherit cmake python-single-r1 virtualx
+
+# rsync: [sender] link_stat "/distfiles/1c/itk-test-bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f" (in gentoo) failed: No such file or directory (2)
+
+MY_PN="InsightToolkit"
+MY_P="${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}
+ 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-doc/doxygen )
+"
+BDEPEND="
+ test? (
+ vtkglue? ( ${VIRTUALX_DEPEND} )
+ python? (
+ $(python_gen_cond_dep 'dev-python/numpy[${PYTHON_USEDEP}]')
+ )
+ )
+"
+
+S="${WORKDIR}/${MY_P}"
+
+PATCHES=(
+ "${FILESDIR}/${PN}-5.2.1-system-tiff-has-64.patch"
+ "${FILESDIR}/${PN}-5.3.0-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 ${ITK_WRAP_DIMS} ]]; then
+ elog "For Python language bindings, you can define the dimensions"
+ elog "you want to create bindings for by setting"
+ elog " ITK_WRAP_DIMS=X;Y;Z..."
+ elog "in make.conf, default is 2;3 for 2D and 3D data"
+ fi
+}
+
+src_prepare() {
+ # drop bundled libs
+ local -a DROPS=(
+ DoubleConversion/src/double-conversion
+ Eigen3/src/itkeigen
+ Expat/src/expat
+ GDCM/src/gdcm
+ JPEG/src/itkjpeg
+ HDF5/src/itkhdf5
+ OpenJPEG/src/openjpeg
+ PNG/src/itkpng
+ TIFF/src/itktiff
+ )
+ local x
+ for x in "${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() {
+ # Failing tests reported upstream:
+ # https://github.com/ntustison/ITKAdaptiveDenoising/issues/13
+ if use vtkglue; then
+ virtx cmake_src_test -E "(AdaptiveNonLocalMeansDenoisingImageFilterTest1|AdaptiveNonLocalMeansDenoisingImageFilterTest2)"
+ else
+ cmake_src_test -E "(AdaptiveNonLocalMeansDenoisingImageFilterTest1|AdaptiveNonLocalMeansDenoisingImageFilterTest2)"
+ fi
+}
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-libs/itk/, sci-libs/itk/files/
@ 2023-05-13 1:31 Horea Christian
0 siblings, 0 replies; 8+ messages in thread
From: Horea Christian @ 2023-05-13 1:31 UTC (permalink / raw
To: gentoo-commits
commit: 3d21154c5c99a552d9a79c651f09de25594a88b0
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sat May 13 01:29:30 2023 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sat May 13 01:30:58 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3d21154c
sci-libs/itk: patch for newer gcc
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-libs/itk/files/itk-5.3.0-uint8.patch | 10 ++++++++++
sci-libs/itk/itk-5.3.0-r1.ebuild | 2 ++
2 files changed, 12 insertions(+)
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/itk-5.3.0-r1.ebuild b/sci-libs/itk/itk-5.3.0-r1.ebuild
index 23f3341a2..29a3da5d0 100644
--- a/sci-libs/itk/itk-5.3.0-r1.ebuild
+++ b/sci-libs/itk/itk-5.3.0-r1.ebuild
@@ -92,9 +92,11 @@ BDEPEND="
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() {
^ permalink raw reply related [flat|nested] 8+ messages in thread
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