sci-libs/itk: trying to solve limits issue

Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Horea Christian <chr@chymera.eu>

sci-libs/itk/ChangeLog

@@ -0,0 +1,12 @@
+*itk-5.1.0 (09 Jan 2022)
+
+  09 Jan 2022;  <chymera@gentoo.org>
+  +files/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch,
+  +files/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch,
+  +files/0003-COMP-Fixed-itkGradientDescentOptimizerv4-wrapping-wa.patch,
+  +files/0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch,
+  +files/0005-make-gdcm-helper-library-static.patch,
+  +files/ITKModuleRemote.patch, +files/itk-5.1.0-downloads.patch,
+  +files/itk-5.1.0-include_limits.patch, +files/nrrdio-linking.patch,
+  +files/tests.patch, +itk-5.1.0.ebuild, +metadata.xml:
+  sci-libs/itk: trying to solve limits issue

sci-libs/itk/Manifest

@@ -0,0 +1,6 @@
+DIST ITKGenericLabelInterpolator-5.1.0.tar.gz 140286 SHA256 84a045540f95a00e07df2123e9b9a7825ad0acece83a929639109a77e95435a1 SHA512 7bf6310e8b0ea2356ae8ce0ddd0bc3a1516aa6bb5e3e8df9ed0114f1bb2b299d2edd046f27dbae364082afc63e225a3691c794c93d347ee564db617ea3fbf489 WHIRLPOOL 0cd7bfde3d18dfbef7a798c4cbb17bf444bfab93b5b4887cdc0d244e2aef07ebe1b1af796f5f49c768af3568d3f96aed6aaaf5d23fb5553cb83b4fc6474b54fe
+DIST InsightData-5.1.0.tar.gz 292322103 SHA256 777f587c587b47d76157a0ee87a5942b944742f334b801abe0e6dc1ad1d8424f SHA512 458c2959ba5e0745eee23e16ff7178230a7bae94d7dff065b3b38136e238becff96554693e3b2149d2307949c23a6c695c92676f8d44e6f7305dbb8bed48c9fa WHIRLPOOL d5785f862c627cabc97c469ac9fb84d1493e1827fd993c68ed5019e7062adc7fe68efe6ab2471c7c6b2a9d542cbfdb1a00c6633fa7be498cbc9e09fa12d3710a
+DIST InsightToolkit-5.1.0.tar.gz 20694338 SHA256 121020a1611508cec8123eb5226215598cec07be627d843a2e6b6da891e61d13 SHA512 413b6ef549b59d8f507038130446ccb704794c6d0980d8ab631d1b1051cb91f399e77c26b69fab6a1e9b9bb4cc233d49996c3ee735cd4de065993d4379b4ed4c WHIRLPOOL bbe7368cc46dc1a0869d8ab47218d0777e689be17114048653a537fbe792dfc0eb0e687b06fa894218cc35ef95143df75a46c17ffd6b072233e9f72a3c811825
+DIST itk-5.1.0-test-a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a 1017 SHA256 d5e1b340676b07c4d08dd8938280c8ec490620a88ae8b3d3798975ed83506985 SHA512 e69c77894cab5b295ec5edbecdf693525ec9a4673810b87cbc28646ea40888b7792b5707840069e277905c8b0014bd84ecea036836f87c3b16f388f544e34341 WHIRLPOOL 2908b4ea8ec516bbe9fd290cd5aa03262418c0028128c0d575e1b855e9dc1af2c818d6c59c879c153f5f02e67ff8cbf902a5e3076dca6dc6d7de3dce28d318bc
+DIST itk-5.1.0-test-bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f 1018 SHA256 339345972050e6fabad649438852811612b80f35626d1b88dd6361296a21b036 SHA512 27952af5d6243aa31c187280ea9ba82c434db3614b3db3b406fe8e5c7e4b7e333bc179d5d9956d5a17aa670a7aa7cfce037d37c4225125e703602e322d8ec68b WHIRLPOOL 47f28fdb11ce0444763f91f7c295f2574da04d11bc6b8fdb65fb0ac35ee97f8d8706e7a20259030bcef517c07c8e6312825ea500d2396c3547836169cdde5491
+DIST itk-5.1.0-testingdata.tar.gz 2409232372 SHA256 bac8365cb56a6c5f68e565445e00012f31453b06e8f7879bc7c3238796a67948 SHA512 8b451608cb3f75d3ba6a78fd23e79495948c2792a98d831e0f0c93745595df84d3c2a8d76389976f67ac7e7e1f5a44a18d201e51d2ee659cdb708ae28536df8f WHIRLPOOL 4c9f65bb51a0714a24db6c1e739fff32b454e0289135cd190146df0fd6dece736ff348d9aeae388dff8ce9ccc9010c979f1a6051065f92bbb0bc98c8628aab4e

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

@@ -0,0 +1,50 @@
+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
+

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

@@ -0,0 +1,28 @@
+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
+

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

@@ -0,0 +1,73 @@
+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
+

sci-libs/itk/files/0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch

@@ -0,0 +1,30 @@
+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()
+

sci-libs/itk/files/0005-make-gdcm-helper-library-static.patch

@@ -0,0 +1,11 @@
+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()

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()

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
+   )

sci-libs/itk/files/itk-5.1.0-include_limits.patch

@@ -0,0 +1,10 @@
+--- 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.h>
+
+ namespace gdcm
+ {

sci-libs/itk/files/nrrdio-linking.patch

@@ -0,0 +1,15 @@
+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})

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()

sci-libs/itk/itk-5.1.0.ebuild

@@ -0,0 +1,191 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{7,8,9} )
+
+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=
+	virtual/jpeg: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 "${S}"/Examples/*
+	fi
+
+	echo "ITK_DATA_ROOT=${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
+		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
+}

sci-libs/itk/metadata.xml

@@ -0,0 +1,24 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>maintainer-wanted@gentoo.org</email>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+	<longdescription lang="en">
+		Insight Segmentation and Registration Toolkit (ITK) is a library
+		that provides developers with an extensive suite of tools for image
+		analysis.
+	</longdescription>
+		<use>
+		<flag name="itkv4-compat">Compatibility for applications using ITKv4 API</flag>
+		<flag name="review">Enable compilation of methods under review</flag>
+		<flag name="vtkglue">PLEASE FIX MY DESCRIPTION</flag>
+	</use>
+	<upstream>
+		<remote-id type="sourceforge">itk</remote-id>
+	</upstream>
+</pkgmetadata>