[gentoo-commits] proj/sci:master commit in: sci-libs/itk/, sci-libs/itk/files/
commit: 3d21154c5c99a552d9a79c651f09de25594a88b0
Author: Horea Christian chymera eu>
AuthorDate: Sat May 13 01:29:30 2023 +
Commit: Horea Christian gmail com>
CommitDate: Sat May 13 01:30:58 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=3d21154c
sci-libs/itk: patch for newer gcc
Signed-off-by: Horea Christian 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 0..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
+ #include "ITKMathematicalMorphologyExport.h"
++#include
+
+
+ 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() {
[gentoo-commits] proj/sci:master commit in: sci-libs/itk/, sci-libs/itk/files/
commit: d23b080b9afe74c6590a9827d505e9234c00deb0
Author: Horea Christian chymera eu>
AuthorDate: Sat Mar 25 01:48:55 2023 +
Commit: Horea Christian gmail com>
CommitDate: Sat Mar 25 01:48:55 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=d23b080b
sci-libs/itk: add 5.3.0
Signed-off-by: Horea Christian 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 0..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
++/* Use the openjpeg library configured for ITK. */
++#cmakedefine ITK_USE_SYSTEM_OPENJPEG
++#ifdef ITK_USE_SYSTEM_OPENJPEG
++# include
++#else
++# include
++#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
[gentoo-commits] proj/sci:master commit in: sci-libs/itk/, sci-libs/itk/files/
commit: 76b20521901742c59aa823035357a3a49ebb0aad
Author: François-Xavier Carton gmail com>
AuthorDate: Thu Sep 29 18:08:30 2022 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Fri Sep 30 06:49:55 2022 +
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 gmail.com>
Closes: https://github.com/gentoo/sci/pull/1172
Signed-off-by: Andrew Ammerlaan 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
@@ -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
+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
+---
+ 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
[gentoo-commits] proj/sci:master commit in: sci-libs/itk/, sci-libs/itk/files/
commit: 9ff3b1053e275f3a30fa574c79f3ee1af8cbeca0
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Thu Sep 15 11:09:45 2022 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Thu Sep 15 11:09:45 2022 +
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 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..0
--- 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
14:30:53.0 -0400
-+++ b/Modules/Remote/GenericLabelInterpolator.remote.cmake 2020-04-25
14:30:53.0 -0400
-@@ -44,6 +44,4 @@
- itk_fetch_module(GenericLabelInterpolator
- "A generic interpolator for multi-label images."
- MODULE_COMPLIANCE_LEVEL 2
-- GIT_REPOSITORY
${git_protocol}://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator.git
-- GIT_TAG b95fe46c7f4fe8002af67c67e6fe4e1f087bf6b7
- )
diff --git a/sci-libs/itk/files/itk-5.1.0-include_limits.patch
b/sci-libs/itk/files/itk-5.1.0-include_limits.patch
deleted file mode 100644
index 9a8fae820..0
--- a/sci-libs/itk/files/itk-5.1.0-include_limits.patch
+++ /dev/null
@@ -1,10 +0,0 @@
a/Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmImageChangePhotometricInterpretation.h
-+++
a/Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmImageChangePhotometricInterpretation.h
-@@ -16,6 +16,7 @@
-
- #include "gdcmImageToImageFilter.h"
- #include "gdcmPhotometricInterpretation.h"
-+#include
-
- namespace gdcm
- {
diff --git a/sci-libs/itk/files/tests.patch b/sci-libs/itk/files/tests.patch
deleted file mode 100644
index c24714e4d..0
--- a/sci-libs/itk/files/tests.patch
+++ /dev/null
@@ -1,41 +0,0 @@
-Known to fail by upstream:
-https://github.com/InsightSoftwareConsortium/ITK/issues/1212#issuecomment-527998115
-
a/Modules/Bridge/VtkGlue/test/CMakeLists.txt 2019-09-09
00:45:14.736032139 +0200
-+++ b/Modules/Bridge/VtkGlue/test/CMakeLists.txt 2019-09-09
00:49:42.183935497 +0200
-@@ -7,8 +7,6 @@
- if(NOT VTK_RENDERING_BACKEND STREQUAL "None")
- list(APPEND ITKVtkGlueTests
- itkVtkMedianFilterTest.cxx
--itkVtkConnectedComponentImageFilterTest.cxx
--QuickViewTest.cxx
- # ### runViewImage ###
- # No test generated. Use it for view images (2D or 3D) with:
- # ITKVtkGlueTestDriver runViewImage image_file
-@@ -40,26 +38,3 @@
- NAME itkVTKImageToImageFilterTest
- COMMAND ITKVtkGlueTestDriver
- itkVTKImageToImageFilterTest)
--
--if(NOT VTK_RENDERING_BACKEND STREQUAL "None")
-- itk_add_test(
--NAME itkVtkMedianImageFilterTest
--COMMAND ITKVtkGlueTestDriver
-- itkVtkMedianFilterTest DATA{${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..0
--- 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
-
[gentoo-commits] proj/sci:master commit in: sci-libs/itk/, sci-libs/itk/files/
commit: e183cbc1d2404c5ce6348627365cdc1aa483c375
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Wed Aug 31 10:30:15 2022 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Wed Aug 31 10:30:15 2022 +
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 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..0
---
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
-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
-
-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 000..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..0
---
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
-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
[gentoo-commits] proj/sci:master commit in: sci-libs/itk/, sci-libs/itk/files/
commit: b4acbb5f52ed06ad45b5a4e877498a6c9f683d4e
Author: François-Xavier Carton gmail com>
AuthorDate: Fri Jun 10 13:16:57 2022 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Tue Aug 23 10:58:09 2022 +
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 gmail.com>
Signed-off-by: Andrew Ammerlaan 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 0..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
+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 0..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
++/* Use the openjpeg library configured for ITK. */
++#cmakedefine ITK_USE_SYSTEM_OPENJPEG
++#ifdef ITK_USE_SYSTEM_OPENJPEG
++# include
++#else
++# include
++#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)
++
[gentoo-commits] proj/sci:master commit in: sci-libs/itk/, sci-libs/itk/files/
commit: 7112647657d76049ee42f5e2c86c05c2c1330760
Author: Horea Christian chymera eu>
AuthorDate: Fri Sep 25 07:33:20 2020 +
Commit: Horea Christian gmail com>
CommitDate: Fri Sep 25 07:33:20 2020 +
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 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 0..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
14:30:53.0 -0400
b/Modules/Remote/GenericLabelInterpolator.remote.cmake 2020-04-25
14:30:53.0 -0400
+@@ -44,6 +44,4 @@
+ itk_fetch_module(GenericLabelInterpolator
+ "A generic interpolator for multi-label images."
+ MODULE_COMPLIANCE_LEVEL 2
+- GIT_REPOSITORY
${git_protocol}://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator.git
+- GIT_TAG b95fe46c7f4fe8002af67c67e6fe4e1f087bf6b7
+ )
diff --git a/sci-libs/itk/itk-5.1.0.ebuild b/sci-libs/itk/itk-5.1.0.ebuild
new file mode 100644
index 0..64fd555cb
--- /dev/null
+++ b/sci-libs/itk/itk-5.1.0.ebuild
@@ -0,0 +1,188 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python2_7 python3_{5,6,7} )
+
+inherit toolchain-funcs cmake python-single-r1
+
+MY_PN="InsightToolkit"
+MY_P="${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 ${ITK_WRAP_DIMS} ]]; then
+ elog "For Python language
[gentoo-commits] proj/sci:master commit in: sci-libs/itk/, sci-libs/itk/files/
commit: 445eb95b61c9b12481b24f962123d0f13e940ab6
Author: Horea Christian chymera eu>
AuthorDate: Mon Sep 9 08:25:49 2019 +
Commit: Horea Christian gmail com>
CommitDate: Mon Sep 9 08:25:49 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=445eb95b
sci-libs/itk: version bump to 5.0.1
And removed deprecated versions on account of gccxml removal
Package-Manager: Portage-2.3.72, Repoman-2.3.17
Signed-off-by: Horea Christian chymera.eu>
sci-libs/itk/files/ITKModuleRemote.patch | 45 ++
sci-libs/itk/files/tests.patch | 41 ++
sci-libs/itk/itk-4.12.0.ebuild | 136 --
sci-libs/itk/itk-4.4.2-r1.ebuild | 135 --
sci-libs/itk/itk-4.4.2.ebuild | 115 ---
sci-libs/itk/itk-4.5.1.ebuild | 155 -
.../itk/{itk-5.0_rc1.ebuild => itk-5.0.1.ebuild} | 50 +--
sci-libs/itk/metadata.xml | 1 -
8 files changed, 124 insertions(+), 554 deletions(-)
diff --git a/sci-libs/itk/files/ITKModuleRemote.patch
b/sci-libs/itk/files/ITKModuleRemote.patch
new file mode 100644
index 0..eb130159a
--- /dev/null
+++ b/sci-libs/itk/files/ITKModuleRemote.patch
@@ -0,0 +1,45 @@
+Disable automatic git clone attempt for modules:
+https://github.com/InsightSoftwareConsortium/ITK/issues/1157
+
+--- a/CMake/ITKModuleRemote.cmake 2019-08-13 18:10:33.385472767 +0200
b/CMake/ITKModuleRemote.cmake 2019-08-13 18:12:04.020198966 +0200
+@@ -165,39 +165,4 @@
+ set(Module_${_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/${_name}"
+- )
+- endif()
+ endfunction()
diff --git a/sci-libs/itk/files/tests.patch b/sci-libs/itk/files/tests.patch
new file mode 100644
index 0..c24714e4d
--- /dev/null
+++ b/sci-libs/itk/files/tests.patch
@@ -0,0 +1,41 @@
+Known to fail by upstream:
+https://github.com/InsightSoftwareConsortium/ITK/issues/1212#issuecomment-527998115
+
+--- a/Modules/Bridge/VtkGlue/test/CMakeLists.txt 2019-09-09
00:45:14.736032139 +0200
b/Modules/Bridge/VtkGlue/test/CMakeLists.txt 2019-09-09
00:49:42.183935497 +0200
+@@ -7,8 +7,6 @@
+ if(NOT VTK_RENDERING_BACKEND STREQUAL "None")
+ list(APPEND ITKVtkGlueTests
+ itkVtkMedianFilterTest.cxx
+-itkVtkConnectedComponentImageFilterTest.cxx
+-QuickViewTest.cxx
+ # ### runViewImage ###
+ # No test generated. Use it for view images (2D or 3D) with:
+ # ITKVtkGlueTestDriver runViewImage image_file
+@@ -40,26 +38,3 @@
+ NAME itkVTKImageToImageFilterTest
+ COMMAND ITKVtkGlueTestDriver
+ itkVTKImageToImageFilterTest)
+-
+-if(NOT VTK_RENDERING_BACKEND STREQUAL "None")
+- itk_add_test(
+-NAME itkVtkMedianImageFilterTest
+-COMMAND ITKVtkGlueTestDriver
+- itkVtkMedianFilterTest DATA{${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
