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SCIInstitute / Seg3D

Seg3D is a free volume segmentation and processing tool developed by the NIH Center for Integrative Biomedical Computing at the University of Utah Scientific Computing and Imaging (SCI) Institute.
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ITK5 migration #384

Closed dzenanz closed 3 years ago

dzenanz commented 3 years ago

This is a cleaned-up version of #382. Closes #382.

tarkpate commented 3 years ago

Here's the build log on linux(gcc 10.2):

[ 40%] Built target Application_Renderer
[ 41%] Built target Application_Tool
[ 42%] Built target Application_ToolManager
[ 42%] Built target Application_Clipboard
[ 47%] Built target Application_Tools
[ 48%] Built target Application_ViewerManager
[ 48%] Built target Application_UndoBuffer
[ 48%] Built target Application_Socket
[ 48%] Building CXX object Application/ImageRegistrationTools/CMakeFiles/Application_ImageRegistrationTools.dir/Actions/ActionAssembleFilter.cc.o
In file included from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/scoped_ptr.hpp:14,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex/v4/regex_workaround.hpp:41,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex/v4/regex.hpp:32,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex.hpp:31,
                 from /home/tpat/repos/seg3d/src/Core/Action/ActionParameter.h:40,
                 from /home/tpat/repos/seg3d/src/Core/Action/Actions.h:37,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.h:32,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.cc:29:
/home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   68 |     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
      |                               ^~~~~~~~
In file included from /usr/include/c++/10.2.0/memory:83,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/smart_ptr/scoped_ptr.hpp:21,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/scoped_ptr.hpp:14,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex/v4/regex_workaround.hpp:41,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex/v4/regex.hpp:32,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex.hpp:31,
                 from /home/tpat/repos/seg3d/src/Core/Action/ActionParameter.h:40,
                 from /home/tpat/repos/seg3d/src/Core/Action/Actions.h:37,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.h:32,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.cc:29:
/usr/include/c++/10.2.0/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/smart_ptr/shared_ptr.hpp:28,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/shared_ptr.hpp:17,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex/v4/regex_workaround.hpp:43,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex/v4/regex.hpp:32,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex.hpp:31,
                 from /home/tpat/repos/seg3d/src/Core/Action/ActionParameter.h:40,
                 from /home/tpat/repos/seg3d/src/Core/Action/Actions.h:37,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.h:32,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.cc:29:
/home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  395 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/10.2.0/memory:83,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/smart_ptr/scoped_ptr.hpp:21,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/scoped_ptr.hpp:14,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex/v4/regex_workaround.hpp:41,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex/v4/regex.hpp:32,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex.hpp:31,
                 from /home/tpat/repos/seg3d/src/Core/Action/ActionParameter.h:40,
                 from /home/tpat/repos/seg3d/src/Core/Action/Actions.h:37,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.h:32,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.cc:29:
/usr/include/c++/10.2.0/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/shared_ptr.hpp:17,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex/v4/regex_workaround.hpp:43,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex/v4/regex.hpp:32,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex.hpp:31,
                 from /home/tpat/repos/seg3d/src/Core/Action/ActionParameter.h:40,
                 from /home/tpat/repos/seg3d/src/Core/Action/Actions.h:37,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.h:32,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.cc:29:
/home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/smart_ptr/shared_ptr.hpp:242:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  242 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
In file included from /usr/include/c++/10.2.0/memory:83,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/smart_ptr/scoped_ptr.hpp:21,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/scoped_ptr.hpp:14,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex/v4/regex_workaround.hpp:41,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex/v4/regex.hpp:32,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex.hpp:31,
                 from /home/tpat/repos/seg3d/src/Core/Action/ActionParameter.h:40,
                 from /home/tpat/repos/seg3d/src/Core/Action/Actions.h:37,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.h:32,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.cc:29:
/usr/include/c++/10.2.0/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/shared_ptr.hpp:17,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex/v4/regex_workaround.hpp:43,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex/v4/regex.hpp:32,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex.hpp:31,
                 from /home/tpat/repos/seg3d/src/Core/Action/ActionParameter.h:40,
                 from /home/tpat/repos/seg3d/src/Core/Action/Actions.h:37,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.h:32,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.cc:29:
/home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/smart_ptr/shared_ptr.hpp:441:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  441 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
In file included from /usr/include/c++/10.2.0/memory:83,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/smart_ptr/scoped_ptr.hpp:21,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/scoped_ptr.hpp:14,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex/v4/regex_workaround.hpp:41,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex/v4/regex.hpp:32,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex.hpp:31,
                 from /home/tpat/repos/seg3d/src/Core/Action/ActionParameter.h:40,
                 from /home/tpat/repos/seg3d/src/Core/Action/Actions.h:37,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.h:32,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.cc:29:
/usr/include/c++/10.2.0/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/shared_ptr.hpp:17,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex/v4/regex_workaround.hpp:43,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex/v4/regex.hpp:32,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex.hpp:31,
                 from /home/tpat/repos/seg3d/src/Core/Action/ActionParameter.h:40,
                 from /home/tpat/repos/seg3d/src/Core/Action/Actions.h:37,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.h:32,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.cc:29:
/home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/smart_ptr/shared_ptr.hpp:454:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  454 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
In file included from /usr/include/c++/10.2.0/memory:83,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/smart_ptr/scoped_ptr.hpp:21,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/scoped_ptr.hpp:14,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex/v4/regex_workaround.hpp:41,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex/v4/regex.hpp:32,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex.hpp:31,
                 from /home/tpat/repos/seg3d/src/Core/Action/ActionParameter.h:40,
                 from /home/tpat/repos/seg3d/src/Core/Action/Actions.h:37,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.h:32,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.cc:29:
/usr/include/c++/10.2.0/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/shared_ptr.hpp:17,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex/v4/regex_workaround.hpp:43,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex/v4/regex.hpp:32,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex.hpp:31,
                 from /home/tpat/repos/seg3d/src/Core/Action/ActionParameter.h:40,
                 from /home/tpat/repos/seg3d/src/Core/Action/Actions.h:37,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.h:32,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.cc:29:
/home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/smart_ptr/shared_ptr.hpp:520:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  520 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/10.2.0/memory:83,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/smart_ptr/scoped_ptr.hpp:21,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/scoped_ptr.hpp:14,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex/v4/regex_workaround.hpp:41,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex/v4/regex.hpp:32,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex.hpp:31,
                 from /home/tpat/repos/seg3d/src/Core/Action/ActionParameter.h:40,
                 from /home/tpat/repos/seg3d/src/Core/Action/Actions.h:37,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.h:32,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.cc:29:
/usr/include/c++/10.2.0/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/shared_ptr.hpp:17,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex/v4/regex_workaround.hpp:43,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex/v4/regex.hpp:32,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex.hpp:31,
                 from /home/tpat/repos/seg3d/src/Core/Action/ActionParameter.h:40,
                 from /home/tpat/repos/seg3d/src/Core/Action/Actions.h:37,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.h:32,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.cc:29:
/home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/smart_ptr/shared_ptr.hpp:529:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  529 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/10.2.0/memory:83,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/smart_ptr/scoped_ptr.hpp:21,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/scoped_ptr.hpp:14,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex/v4/regex_workaround.hpp:41,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex/v4/regex.hpp:32,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex.hpp:31,
                 from /home/tpat/repos/seg3d/src/Core/Action/ActionParameter.h:40,
                 from /home/tpat/repos/seg3d/src/Core/Action/Actions.h:37,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.h:32,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.cc:29:
/usr/include/c++/10.2.0/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/shared_ptr.hpp:17,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex/v4/regex_workaround.hpp:43,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex/v4/regex.hpp:32,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex.hpp:31,
                 from /home/tpat/repos/seg3d/src/Core/Action/ActionParameter.h:40,
                 from /home/tpat/repos/seg3d/src/Core/Action/Actions.h:37,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.h:32,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.cc:29:
/home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/smart_ptr/shared_ptr.hpp:531:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  531 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from /usr/include/c++/10.2.0/memory:83,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/smart_ptr/scoped_ptr.hpp:21,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/scoped_ptr.hpp:14,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex/v4/regex_workaround.hpp:41,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex/v4/regex.hpp:32,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex.hpp:31,
                 from /home/tpat/repos/seg3d/src/Core/Action/ActionParameter.h:40,
                 from /home/tpat/repos/seg3d/src/Core/Action/Actions.h:37,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.h:32,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.cc:29:
/usr/include/c++/10.2.0/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/bind/mem_fn.hpp:25,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/mem_fn.hpp:22,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/bind/bind.hpp:26,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/bind.hpp:22,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/thread/detail/thread.hpp:30,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/thread/thread_only.hpp:22,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/thread/thread.hpp:12,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/thread.hpp:13,
                 from /home/tpat/repos/seg3d/src/Core/Action/ActionInfo.h:42,
                 from /home/tpat/repos/seg3d/src/Core/Action/Action.h:45,
                 from /home/tpat/repos/seg3d/src/Core/Action/Actions.h:39,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.h:32,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.cc:29:
/home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/get_pointer.hpp: At global scope:
/home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/get_pointer.hpp:27:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   27 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
      |                                        ^~~~~~~~
In file included from /usr/include/c++/10.2.0/memory:83,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/smart_ptr/scoped_ptr.hpp:21,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/scoped_ptr.hpp:14,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex/v4/regex_workaround.hpp:41,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex/v4/regex.hpp:32,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex.hpp:31,
                 from /home/tpat/repos/seg3d/src/Core/Action/ActionParameter.h:40,
                 from /home/tpat/repos/seg3d/src/Core/Action/Actions.h:37,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.h:32,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.cc:29:
/usr/include/c++/10.2.0/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/thread/thread.hpp:13,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/thread.hpp:13,
                 from /home/tpat/repos/seg3d/src/Core/Action/ActionInfo.h:42,
                 from /home/tpat/repos/seg3d/src/Core/Action/Action.h:45,
                 from /home/tpat/repos/seg3d/src/Core/Action/Actions.h:39,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.h:32,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.cc:29:
/home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/thread/detail/thread_group.hpp: In member function ‘boost::thread* boost::thread_group::create_thread(F)’:
/home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/thread/detail/thread_group.hpp:78:18: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   78 |             std::auto_ptr<thread> new_thread(new thread(threadfunc));
      |                  ^~~~~~~~
In file included from /usr/include/c++/10.2.0/memory:83,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/smart_ptr/scoped_ptr.hpp:21,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/scoped_ptr.hpp:14,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex/v4/regex_workaround.hpp:41,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex/v4/regex.hpp:32,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/regex.hpp:31,
                 from /home/tpat/repos/seg3d/src/Core/Action/ActionParameter.h:40,
                 from /home/tpat/repos/seg3d/src/Core/Action/Actions.h:37,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.h:32,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.cc:29:
/usr/include/c++/10.2.0/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/mpl/arg.hpp:25,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/variant/variant_fwd.hpp:19,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/variant/detail/apply_visitor_delayed.hpp:20,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/variant/apply_visitor.hpp:18,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/signals2/slot_base.hpp:21,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/signals2/detail/tracked_objects_visitor.hpp:18,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/signals2/slot.hpp:22,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/signals2/connection.hpp:23,
                 from /home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/signals2/signal.hpp:22,
                 from /home/tpat/repos/seg3d/src/Core/Action/ActionDispatcher.h:38,
                 from /home/tpat/repos/seg3d/src/Core/Action/Actions.h:43,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.h:32,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.cc:29:
/home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/mpl/assert.hpp: At global scope:
/home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  188 | failed ************ (Pred::************
      |                     ^
/home/tpat/repos/seg3d/bin/Externals/Source/Boost_external/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  193 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.cc:33:
/home/tpat/repos/seg3d/src/Core/ITKCommon/Optimizers/itkImageMosaicVarianceMetric.h:177:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  177 |   virtual void Initialize() throw (ExceptionObject);
      |                             ^~~~~
In file included from /home/tpat/repos/seg3d/src/Core/ITKCommon/Optimizers/itkImageMosaicVarianceMetric.h:315,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.cc:33:
/home/tpat/repos/seg3d/src/Core/ITKCommon/Optimizers/itkImageMosaicVarianceMetric.txx:191:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  191 | Initialize() throw (ExceptionObject)
      |              ^~~~~
In file included from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.cc:32:
/home/tpat/repos/seg3d/src/Core/ITKCommon/common.hxx: In instantiation of ‘bool calc_mosaic_bboxes(const std::vector<T>&, const std::vector<T>&, const std::vector<T>&, std::vector<T>&, std::vector<T>&, unsigned int) [with point_t = itk::Point<double, 2>; transform_pointer_t = itk::SmartPointer<itk::Transform<double, 2, 2> >]’:
/home/tpat/repos/seg3d/src/Core/ITKCommon/common.hxx:2400:51:   required from ‘void calc_mosaic_bbox_load_images(const std::vector<T>&, const std::__cxx11::list<boost::filesystem::path>&, typename image_pointer_t::ObjectType::PointType&, typename image_pointer_t::ObjectType::PointType&, std::vector<typename image_pointer_t::ObjectType::PointType>&, std::vector<typename image_pointer_t::ObjectType::PointType>&, unsigned int, double, unsigned int) [with image_pointer_t = itk::SmartPointer<const itk::Image<float, 2> >; transform_pointer_t = itk::SmartPointer<itk::Transform<double, 2, 2> >; typename image_pointer_t::ObjectType::PointType = itk::Point<double, 2>]’
/home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.cc:364:30:   required from here
/home/tpat/repos/seg3d/src/Core/ITKCommon/common.hxx:2267:11: warning: unused variable ‘image_point’ [-Wunused-variable]
 2267 |   point_t image_point;
      |           ^~~~~~~~~~~
/home/tpat/repos/seg3d/src/Core/ITKCommon/common.hxx:2268:11: warning: unused variable ‘mosaic_point’ [-Wunused-variable]
 2268 |   point_t mosaic_point;
      |           ^~~~~~~~~~~~
/home/tpat/repos/seg3d/src/Core/ITKCommon/common.hxx: In instantiation of ‘void save_image_tile(T*, const boost::filesystem::path&, unsigned int, unsigned int, unsigned int, unsigned int, unsigned int, unsigned int, bool) [with T = itk::Image<float, 2>]’:
/home/tpat/repos/seg3d/src/Core/ITKCommon/common.hxx:1603:27:   required from ‘bool save_as_tiles(T*, const boost::filesystem::path&, const boost::filesystem::path&, unsigned int, unsigned int, double, bool, bool) [with T = itk::Image<float, 2>]’
/home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.cc:628:44:   required from here
/home/tpat/repos/seg3d/src/Core/ITKCommon/common.hxx:1471:24: warning: variable ‘mosaicSize’ set but not used [-Wunused-but-set-variable]
 1471 |   typename T::SizeType mosaicSize = mosaicRegion.GetSize();
      |                        ^~~~~~~~~~
/home/tpat/repos/seg3d/src/Core/ITKCommon/common.hxx: In instantiation of ‘void save_image_tile(T*, const boost::filesystem::path&, unsigned int, unsigned int, unsigned int, unsigned int, unsigned int, unsigned int, bool) [with T = itk::Image<short unsigned int, 2>]’:
/home/tpat/repos/seg3d/src/Core/ITKCommon/common.hxx:1603:27:   required from ‘bool save_as_tiles(T*, const boost::filesystem::path&, const boost::filesystem::path&, unsigned int, unsigned int, double, bool, bool) [with T = itk::Image<short unsigned int, 2>]’
/home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.cc:645:51:   required from here
/home/tpat/repos/seg3d/src/Core/ITKCommon/common.hxx:1471:24: warning: variable ‘mosaicSize’ set but not used [-Wunused-but-set-variable]
/home/tpat/repos/seg3d/src/Core/ITKCommon/common.hxx: In instantiation of ‘void save_image_tile(T*, const boost::filesystem::path&, unsigned int, unsigned int, unsigned int, unsigned int, unsigned int, unsigned int, bool) [with T = itk::Image<short int, 2>]’:
/home/tpat/repos/seg3d/src/Core/ITKCommon/common.hxx:1603:27:   required from ‘bool save_as_tiles(T*, const boost::filesystem::path&, const boost::filesystem::path&, unsigned int, unsigned int, double, bool, bool) [with T = itk::Image<short int, 2>]’
/home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.cc:662:50:   required from here
/home/tpat/repos/seg3d/src/Core/ITKCommon/common.hxx:1471:24: warning: variable ‘mosaicSize’ set but not used [-Wunused-but-set-variable]
/home/tpat/repos/seg3d/src/Core/ITKCommon/common.hxx: In instantiation of ‘void save_image_tile(T*, const boost::filesystem::path&, unsigned int, unsigned int, unsigned int, unsigned int, unsigned int, unsigned int, bool) [with T = itk::Image<unsigned char, 2>]’:
/home/tpat/repos/seg3d/src/Core/ITKCommon/common.hxx:1603:27:   required from ‘bool save_as_tiles(T*, const boost::filesystem::path&, const boost::filesystem::path&, unsigned int, unsigned int, double, bool, bool) [with T = itk::Image<unsigned char, 2>]’
/home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.cc:678:51:   required from here
/home/tpat/repos/seg3d/src/Core/ITKCommon/common.hxx:1471:24: warning: variable ‘mosaicSize’ set but not used [-Wunused-but-set-variable]
In file included from /home/tpat/repos/seg3d/src/Core/ITKCommon/Optimizers/itkImageMosaicVarianceMetric.h:315,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.cc:33:
/home/tpat/repos/seg3d/src/Core/ITKCommon/Optimizers/itkImageMosaicVarianceMetric.txx: In instantiation of ‘void itk::ImageMosaicVarianceMetric<TImage, TInterpolator>::GetValueAndDerivative(const params_t&, itk::ImageMosaicVarianceMetric<TImage, TInterpolator>::measure_t&, itk::ImageMosaicVarianceMetric<TImage, TInterpolator>::derivative_t&) const [with TImage = itk::Image<float, 2>; TInterpolator = itk::LinearInterpolateImageFunction<itk::Image<float, 2>, double>; itk::ImageMosaicVarianceMetric<TImage, TInterpolator>::params_t = itk::OptimizerParameters<double>; itk::ImageMosaicVarianceMetric<TImage, TInterpolator>::measure_t = double; itk::ImageMosaicVarianceMetric<TImage, TInterpolator>::derivative_t = itk::Array<double>]’:
/home/tpat/repos/seg3d/src/Core/ITKCommon/Optimizers/itkImageMosaicVarianceMetric.txx:276:1:   required from here
/home/tpat/repos/seg3d/src/Core/ITKCommon/Optimizers/itkImageMosaicVarianceMetric.txx:435:59: error: cannot bind non-const lvalue reference of type ‘itk::Transform<double, 2, 2>::JacobianPositionType&’ {aka ‘vnl_matrix_fixed<double, 2, 2>&’} to an rvalue of type ‘itk::Transform<double, 2, 2>::JacobianPositionType’ {aka ‘vnl_matrix_fixed<double, 2, 2>’}
  435 |       t->ComputeJacobianWithRespectToPosition(point, data.J_);
      |                                                      ~~~~~^~
In file included from /home/tpat/repos/seg3d/bin/Externals/Install/ITK_external/include/ITK-5.2/vnl/vnl_matrix_fixed.hxx:9,
                 from /home/tpat/repos/seg3d/bin/Externals/Install/ITK_external/include/ITK-5.2/itkMatrix.h:25,
                 from /home/tpat/repos/seg3d/bin/Externals/Install/ITK_external/include/ITK-5.2/itkImageBase.h:34,
                 from /home/tpat/repos/seg3d/bin/Externals/Install/ITK_external/include/ITK-5.2/itkNeighborhoodAccessorFunctor.h:22,
                 from /home/tpat/repos/seg3d/bin/Externals/Install/ITK_external/include/ITK-5.2/itkImage.h:28,
                 from /home/tpat/repos/seg3d/bin/Externals/Install/ITK_external/include/ITK-5.2/itkImageSource.h:32,
                 from /home/tpat/repos/seg3d/bin/Externals/Install/ITK_external/include/ITK-5.2/itkImageToImageFilter.h:31,
                 from /home/tpat/repos/seg3d/src/Core/ITKCommon/Filtering/itkNormalizeImageFilterWithMask.h:40,
                 from /home/tpat/repos/seg3d/src/Core/ITKCommon/common.hxx:47,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.cc:32:
/home/tpat/repos/seg3d/bin/Externals/Install/ITK_external/include/ITK-5.2/vnl/vnl_matrix_fixed.h:157:3: note:   after user-defined conversion: ‘vnl_matrix_fixed<T, num_rows, num_cols>::vnl_matrix_fixed(const vnl_matrix<T>&) [with T = double; unsigned int num_rows = 2; unsigned int num_cols = 2]’
  157 |   vnl_matrix_fixed(const vnl_matrix<T>& rhs)
      |   ^~~~~~~~~~~~~~~~
In file included from /home/tpat/repos/seg3d/bin/Externals/Install/ITK_external/include/ITK-5.2/itkMatrixOffsetTransformBase.h:24,
                 from /home/tpat/repos/seg3d/bin/Externals/Install/ITK_external/include/ITK-5.2/itkAffineTransform.h:21,
                 from /home/tpat/repos/seg3d/bin/Externals/Install/ITK_external/include/ITK-5.2/itkSpatialObject.h:30,
                 from /home/tpat/repos/seg3d/src/Core/ITKCommon/Filtering/itkNormalizeImageFilterWithMask.h:42,
                 from /home/tpat/repos/seg3d/src/Core/ITKCommon/common.hxx:47,
                 from /home/tpat/repos/seg3d/src/Application/ImageRegistrationTools/Actions/ActionAssembleFilter.cc:32:
/home/tpat/repos/seg3d/bin/Externals/Install/ITK_external/include/ITK-5.2/itkTransform.h:525:40: note:   initializing argument 2 of ‘void itk::Transform<TParametersValueType, NInputDimensions, NOutputDimensions>::ComputeJacobianWithRespectToPosition(const InputPointType&, itk::Transform<TParametersValueType, NInputDimensions, NOutputDimensions>::JacobianPositionType&) const [with TParametersValueType = double; unsigned int NInputDimensions = 2; unsigned int NOutputDimensions = 2; itk::Transform<TParametersValueType, NInputDimensions, NOutputDimensions>::InputPointType = itk::Point<double, 2>; itk::Transform<TParametersValueType, NInputDimensions, NOutputDimensions>::JacobianPositionType = vnl_matrix_fixed<double, 2, 2>]’
  525 |                                        JacobianPositionType & itkNotUsed(jacobian)) const
      |                                        ^~~~~~~~~~~~~~~~~~~~~~
make[2]: *** [Application/ImageRegistrationTools/CMakeFiles/Application_ImageRegistrationTools.dir/build.make:238: Application/ImageRegistrationTools/CMakeFiles/Application_ImageRegistrationTools.dir/Actions/ActionAssembleFilter.cc.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:2747: Application/ImageRegistrationTools/CMakeFiles/Application_ImageRegistrationTools.dir/all] Error 2
make: *** [Makefile:125: all] Error 2
dzenanz commented 3 years ago

@RubioJr That error appears with non-default option BUILD_MOSAIC_TOOLS. I just pushed a commit which fixes it for me. By the way, Visual Studio provides a much clearer error message in this case: M:\Dev\Seg3D\src\Core/ITKCommon/Optimizers/itkImageMosaicVarianceMetric.txx(435,1): error C2664: 'void itk::Transform<TParametersValueType,2,2>::ComputeJacobianWithRespectToPosition(const itk::Point<double,2> &,vnl_matrix_fixed<double,2,2> &) const': cannot convert argument 2 from 'itk::Array2D<double>' to 'vnl_matrix_fixed<double,2,2> &'

dzenanz commented 3 years ago

@allywarner I cherry-picked your revert of nullptr changes to DatabaseManager into this branch. I believe #382 can be closed/abandoned now.

dcwhite commented 3 years ago

Re: Mac-build github build error, they (Github build farm) updated to the latest XCode and now Seg3d's ancient Python and Boost dependencies don't compile. There's an issue for that already, #315.

tarkpate commented 3 years ago

The build works now on my linux machine now.

dzenanz commented 3 years ago

@RubioJr9 I just applied all your suggestions in a new commit.

dzenanz commented 3 years ago

I force-pushed to this branch to retain the const-related suggestion. Loop unrolling is now in my fork's branch. As that commit contains a lot of whitespace trimming done in this branch, rebasing on current master causes conflicts. I will make a new PR once this PR is merged. This should avoid confusion.

dcwhite commented 3 years ago

Sounds good, thanks a lot

tarkpate commented 3 years ago

Thanks, @dzenanz! The mac build is showing a failure related to python. Would you like me to test a mac build on my local machine?

dzenanz commented 3 years ago

@RubioJr9 yes! Python build fails on my local machine too (unable to include python.h I think). It is unrelated to this PR, it fails the same way with current master.

jessdtate commented 3 years ago

The python crash is likely related to the new clang version used in github actions. We can deal with it in a new PR if it builds on other mac machines.

jessdtate commented 3 years ago

I have this building with clang 11, but it is crashing due a previous opengl problem. If @RubioJr9 and @allywarner can build and run it, let's merge it.

tarkpate commented 3 years ago

@jessdtate It built fine on my machine. I'm running 10.14 with clang 10.0.1.

allywarner commented 3 years ago

@jessdtate also builds for me on 10.14.6.

dcwhite commented 3 years ago

Let's merge this and then immediately fix #385.

dzenanz commented 3 years ago

Hooray!😄

jcfr commented 3 years ago

:100: