Release 5.4 update gdcm

Modules/ThirdParty/GDCM/UpdateFromUpstream.sh

@@ -33,7 +33,6 @@ readonly paths="
   Utilities/gdcm_openjpeg.h
   Utilities/gdcmopenjpeg
   Utilities/gdcmrle
-  Utilities/gdcmutfcpp
   Utilities/gdcmuuid
   Utilities/gdcm_uuid.h
   Utilities/gdcm_zlib.h

Modules/ThirdParty/GDCM/src/gdcm/CMakeLists.txt

@@ -1,14 +1,7 @@
-cmake_minimum_required(VERSION 3.9.2 FATAL_ERROR)
+set(GDCM_MAX_VALIDATED_CMAKE_VERSION "3.13.4")
 
-set(GDCM_MAX_VALIDATED_CMAKE_VERSION "3.13.1")
-if("${CMAKE_VERSION}" VERSION_LESS_EQUAL "${GDCM_MAX_VALIDATED_CMAKE_VERSION}")
-  # As of 2018-12-04 GDCM has been validated to build with cmake version 3.13.1 new policies.
-  # Set and use the newest cmake policies that are validated to work
-  set(GDCM_CMAKE_POLICY_VERSION "${CMAKE_VERSION}")
-else()
-  set(GDCM_CMAKE_POLICY_VERSION "${GDCM_MAX_VALIDATED_CMAKE_VERSION}")
-endif()
-cmake_policy(VERSION ${GDCM_CMAKE_POLICY_VERSION})
+# Set minimum required version of CMake, and policy version
+cmake_minimum_required(VERSION 3.9.2...${GDCM_MAX_VALIDATED_CMAKE_VERSION} FATAL_ERROR) # travis-ci wants 3.9.2
 
 # GDCM version 3.0.0 will only support C++11 and greater
 if(CMAKE_CXX_STANDARD EQUAL "98" )
@@ -17,7 +10,7 @@ endif()
 #----------------------------------------------------------------------------
 
 project(GDCM
-  VERSION 3.0.24
+  VERSION 3.2.5
   LANGUAGES CXX C
 )
 ## NOTE: the "DESCRIPTION" feature of project() was introduced in cmake 3.10.0
@@ -125,20 +118,39 @@ if(BUILD_SHARED_LIBS)
 endif()
 
 #-----------------------------------------------------------------------------
-if(NOT EXECUTABLE_OUTPUT_PATH)
-  set(EXECUTABLE_OUTPUT_PATH ${GDCM_BINARY_DIR}/bin CACHE PATH "Single output directory for building all executables.")
-  mark_as_advanced(EXECUTABLE_OUTPUT_PATH)
+# Compatibility with older usage of EXECUTABLE_OUTPUT_PATH and LIBRARY_OUTPUT_PATH.
+# This should be removed in the future.
+if(EXECUTABLE_OUTPUT_PATH)
+  set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${EXECUTABLE_OUTPUT_PATH})
+  message(WARNING "EXECUTABLE_OUTPUT_PATH is deprecated. Use CMAKE_RUNTIME_OUTPUT_DIRECTORY instead.")
 endif()
-if(NOT LIBRARY_OUTPUT_PATH)
-  set(LIBRARY_OUTPUT_PATH ${GDCM_BINARY_DIR}/bin CACHE PATH "Single output directory for building all libraries.")
-  mark_as_advanced(LIBRARY_OUTPUT_PATH)
+if(LIBRARY_OUTPUT_PATH)
+  set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${LIBRARY_OUTPUT_PATH})
+  set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${LIBRARY_OUTPUT_PATH})
+  message(WARNING "LIBRARY_OUTPUT_PATH is deprecated. Use CMAKE_LIBRARY_OUTPUT_DIRECTORY and CMAKE_ARCHIVE_OUTPUT_DIRECTORY instead.")
 endif()
 
-# TODO: The following should be used for CMake 3 and beyond,
-# EXECUTABLE_OUTPUT_PATH and LIBRARY_OUTPUT_PATH are deprecated
-set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${EXECUTABLE_OUTPUT_PATH})
-set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${LIBRARY_OUTPUT_PATH})
-set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${LIBRARY_OUTPUT_PATH})
+if(NOT CMAKE_RUNTIME_OUTPUT_DIRECTORY)
+  set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/bin)
+endif()
+if(NOT CMAKE_LIBRARY_OUTPUT_DIRECTORY)
+  set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/bin)
+endif()
+if(NOT CMAKE_ARCHIVE_OUTPUT_DIRECTORY)
+  set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/bin)
+endif()
+
+# Set for legacy internal usage of EXECUTABLE_OUTPUT_PATH and LIBRARY_OUTPUT_PATH
+if (NOT EXECUTABLE_OUTPUT_PATH)
+  set(EXECUTABLE_OUTPUT_PATH ${CMAKE_RUNTIME_OUTPUT_DIRECTORY})
+endif()
+if (NOT LIBRARY_OUTPUT_PATH)
+  if (BUILD_SHARED_LIBS)
+    set(LIBRARY_OUTPUT_PATH ${CMAKE_LIBRARY_OUTPUT_DIRECTORY})
+  else()
+    set(LIBRARY_OUTPUT_PATH ${CMAKE_ARCHIVE_OUTPUT_DIRECTORY})
+  endif()
+endif()
 
 #-----------------------------------------------------------------------------
 # Adding GDCM_DATA_ROOT
@@ -187,6 +199,10 @@ macro(CHECK_INCLUDE_FILE_CONCAT FILE VARIABLE)
   endif()
 endmacro()
 
+if(UNIX)
+  include(GNUInstallDirs)
+endif()
+
 #include(${GDCM_SOURCE_DIR}/CMake/gdcmPlatformCxxTests.cmake)
 #
 #GDCM_PLATFORM_CXX_TEST(GDCM_CXX_HAS_FUNCTION
@@ -524,7 +540,7 @@ if(GDCM_STANDALONE)
   endif()
   if(NOT DEFINED GDCM_DEFAULT_JAVA_VERSION)
     # override with cmake -DGDCM_DEFAULT_JAVA_VERSION:STRING=1.5 if you dare
-    set(GDCM_DEFAULT_JAVA_VERSION 1.7)
+    set(GDCM_DEFAULT_JAVA_VERSION 1.8)
   endif()
   if(GDCM_WRAP_JAVA)
     set(GDCM_JAVA_SOURCE_VERSION "${GDCM_DEFAULT_JAVA_VERSION}" CACHE STRING "javac source version")
@@ -696,23 +712,45 @@ if(GDCM_STANDALONE)
       )
 
       # documented at https://vtk.org/doc/nightly/html/group__module.html
-      vtk_module_build(
-        MODULES               ${vtkgdcm_modules}
-        INSTALL_EXPORT        GDCM
-        ARCHIVE_DESTINATION   "${GDCM_INSTALL_LIB_DIR}"
-        HEADERS_DESTINATION   "${GDCM_INSTALL_INCLUDE_DIR}/vtk${vtk_version_suffix}"
-        CMAKE_DESTINATION     "${GDCM_INSTALL_PACKAGE_DIR}"
-        LICENSE_DESTINATION   "${GDCM_INSTALL_DATA_DIR}/vtkgdcm-${GDCM_SHORT_VERSION}"
-        HIERARCHY_DESTINATION "${GDCM_INSTALL_LIB_DIR}/vtk${vtk_version_suffix}/hierarchy/vtkgdcm"
-        LIBRARY_NAME_SUFFIX   "${vtkgdcm_library_suffix}"
-        VERSION               "${GDCM_VERSION}"
-        SOVERSION             "1"
-        # TODO: these are probably not set as they should be
-        #USE_EXTERNAL          "${GDCM_USE_EXTERNAL}"
-        #TEST_DATA_TARGET      vtkgdcmData
-        #TEST_INPUT_DATA_DIRECTORY  "${vtkgdcm_test_data_directory_input}"
-        #TEST_OUTPUT_DATA_DIRECTORY "${vtkgdcm_test_data_directory_output}"
-      )
+      if(VTK_VERSION VERSION_LESS 9.3)
+        vtk_module_build(
+          MODULES               ${vtkgdcm_modules}
+          INSTALL_EXPORT        GDCM
+          ARCHIVE_DESTINATION   "${GDCM_INSTALL_LIB_DIR}"
+          HEADERS_DESTINATION   "${GDCM_INSTALL_INCLUDE_DIR}/vtk${vtk_version_suffix}"
+          CMAKE_DESTINATION     "${GDCM_INSTALL_PACKAGE_DIR}"
+          LICENSE_DESTINATION   "${GDCM_INSTALL_DATA_DIR}/vtkgdcm-${GDCM_SHORT_VERSION}"
+          #SPDX_DESTINATION      "${GDCM_INSTALL_DATA_DIR}/vtkgdcm-${GDCM_SHORT_VERSION}"
+          HIERARCHY_DESTINATION "${GDCM_INSTALL_LIB_DIR}/vtk${vtk_version_suffix}/hierarchy/vtkgdcm"
+          LIBRARY_NAME_SUFFIX   "${vtkgdcm_library_suffix}"
+          VERSION               "${GDCM_VERSION}"
+          SOVERSION             "1"
+          # TODO: these are probably not set as they should be
+          #USE_EXTERNAL          "${GDCM_USE_EXTERNAL}"
+          #TEST_DATA_TARGET      vtkgdcmData
+          #TEST_INPUT_DATA_DIRECTORY  "${vtkgdcm_test_data_directory_input}"
+          #TEST_OUTPUT_DATA_DIRECTORY "${vtkgdcm_test_data_directory_output}"
+        )
+      else()
+        vtk_module_build(
+          MODULES               ${vtkgdcm_modules}
+          INSTALL_EXPORT        GDCM
+          ARCHIVE_DESTINATION   "${GDCM_INSTALL_LIB_DIR}"
+          HEADERS_DESTINATION   "${GDCM_INSTALL_INCLUDE_DIR}/vtk${vtk_version_suffix}"
+          CMAKE_DESTINATION     "${GDCM_INSTALL_PACKAGE_DIR}"
+          LICENSE_DESTINATION   "${GDCM_INSTALL_DATA_DIR}/vtkgdcm-${GDCM_SHORT_VERSION}"
+          SPDX_DESTINATION      "${GDCM_INSTALL_DATA_DIR}/vtkgdcm-${GDCM_SHORT_VERSION}"
+          HIERARCHY_DESTINATION "${GDCM_INSTALL_LIB_DIR}/vtk${vtk_version_suffix}/hierarchy/vtkgdcm"
+          LIBRARY_NAME_SUFFIX   "${vtkgdcm_library_suffix}"
+          VERSION               "${GDCM_VERSION}"
+          SOVERSION             "1"
+          # TODO: these are probably not set as they should be
+          #USE_EXTERNAL          "${GDCM_USE_EXTERNAL}"
+          #TEST_DATA_TARGET      vtkgdcmData
+          #TEST_INPUT_DATA_DIRECTORY  "${vtkgdcm_test_data_directory_input}"
+          #TEST_OUTPUT_DATA_DIRECTORY "${vtkgdcm_test_data_directory_output}"
+        )
+      endif()
 
       if(VTKGDCM_WRAP_PYTHON)
         find_package(PythonInterp ${VTK_PYTHON_VERSION} QUIET)

Modules/ThirdParty/GDCM/src/gdcm/Source/Common/gdcmASN1.cxx

@@ -73,7 +73,7 @@ bool ASN1::ParseDump(const char *array, size_t length)
   BIO *out=NULL;
 
   out=BIO_new(BIO_s_file());
-  assert( out );
+  gdcm_assert( out );
   BIO_set_fp(out,stdout,BIO_NOCLOSE|BIO_FP_TEXT);
   if (!ASN1_parse_dump(out,(const unsigned char*)array,length,indent,dump) )
     {

Modules/ThirdParty/GDCM/src/gdcm/Source/Common/gdcmBoxRegion.cxx

@@ -67,7 +67,7 @@ Region *BoxRegion::Clone() const
 
 bool BoxRegion::Empty() const
 {
-  assert( 0 );
+  gdcm_assert( 0 );
   return false;
 }
 
@@ -146,14 +146,14 @@ BoxRegion BoxRegion::BoundingBox(BoxRegion const & b1, BoxRegion const & b2 )
 
 BoxRegion::BoxRegion(const BoxRegion& b)
 {
-  assert( b.Internals );
+  gdcm_assert( b.Internals );
   Internals = new BoxRegionInternals;
   *Internals = *b.Internals;
 }
 
 void BoxRegion::operator=(const BoxRegion& b)
 {
-  assert( b.Internals );
+  gdcm_assert( b.Internals );
   *Internals = *b.Internals;
 }
 

Modules/ThirdParty/GDCM/src/gdcm/Source/Common/gdcmCAPICryptographicMessageSyntax.cxx

@@ -313,7 +313,7 @@ bool CAPICryptographicMessageSyntax::Decrypt(char *output, size_t &outlen, const
   keyBlob.header.reserved = 0;
   keyBlob.header.aiKeyAlg = GetAlgIdByObjId(cekAlg->pszObjId);
   keyBlob.cbKeySize = cekLen;
-  assert(cekLen <= 32);
+  gdcm_assert(cekLen <= 32);
   memcpy(keyBlob.rgbKeyData, cek, cekLen);
 
   if (!CryptImportKey(hProv, (unsigned char*)&keyBlob, sizeof(keyBlob), 0, 0, &hCEK))
@@ -480,7 +480,7 @@ void CAPICryptographicMessageSyntax::ReverseBytes(unsigned char* data, DWORD len
 
 bool CAPICryptographicMessageSyntax::LoadFile(const char * filename, unsigned char* & buffer, DWORD & bufLen)
 {
-  assert( !buffer );
+  gdcm_assert( !buffer );
   FILE * f = fopen(filename, "rb");
   if (f == NULL)
     {

Modules/ThirdParty/GDCM/src/gdcm/Source/Common/gdcmCommand.h

@@ -115,7 +115,7 @@ class MemberCommand : public Command
   T* m_This;
   TMemberFunctionPointer m_MemberFunction;
   TConstMemberFunctionPointer m_ConstMemberFunction;
-  MemberCommand():m_MemberFunction(nullptr),m_ConstMemberFunction(nullptr) {}
+  MemberCommand():m_This(nullptr),m_MemberFunction(nullptr),m_ConstMemberFunction(nullptr) {}
   ~MemberCommand() override= default;
 
 };

Modules/ThirdParty/GDCM/src/gdcm/Source/Common/gdcmCryptoFactory.cxx

@@ -61,7 +61,7 @@ CryptoFactory* CryptoFactory::GetFactoryInstance(CryptoLib id)
     gdcmErrorMacro( "No crypto factory registered with id " << (int)id );
     return nullptr;
     }
-  assert(it->second);
+  gdcm_assert(it->second);
   return it->second;
 }
 

Modules/ThirdParty/GDCM/src/gdcm/Source/Common/gdcmDataEvent.h

@@ -29,7 +29,7 @@ class DataEvent : public AnyEvent
   typedef AnyEvent Superclass;
   DataEvent(const char *bytes = nullptr, size_t len = 0):Bytes(bytes),Length(len) {}
   ~DataEvent() override = default;
-  DataEvent(const Self&s) : AnyEvent(s){};
+  DataEvent(const Self&s) : AnyEvent(s), Bytes(nullptr), Length(0) {}
   void operator=(const Self&) = delete;
 
   const char * GetEventName() const override { return "DataEvent"; }

Modules/ThirdParty/GDCM/src/gdcm/Source/Common/gdcmDirectory.cxx

@@ -68,7 +68,7 @@ unsigned int Directory::Explore(FilenameType const &name, bool recursive)
   if ('\\' == dirName[dirName.size() - 1])
     dirName = dirName.substr(0, dirName.size() - 1);
   if ('/' != dirName[dirName.size() - 1]) dirName.push_back('/');
-  assert( '/' == dirName[dirName.size()-1] );
+  gdcm_assert( '/' == dirName[dirName.size()-1] );
   const std::wstring firstfile = dirName+L"*";
   HANDLE hFile = FindFirstFileW(firstfile.c_str(), &fileData);
 
@@ -106,7 +106,7 @@ unsigned int Directory::Explore(FilenameType const &name, bool recursive)
 #else
   std::string fileName;
   std::string dirName = name;
-  // assert( System::FileIsDirectory( dirName ) );
+  // gdcm_assert( System::FileIsDirectory( dirName ) );
   Directories.push_back(dirName);
   // Real POSIX implementation: scandir is a BSD extension only, and doesn't
   // work on debian for example
@@ -127,7 +127,7 @@ unsigned int Directory::Explore(FilenameType const &name, bool recursive)
   struct stat buf;
   dirent *d;
   if ('/' != dirName[dirName.size()-1]) dirName.push_back('/');
-  assert( '/' == dirName[dirName.size()-1] );
+  gdcm_assert( '/' == dirName[dirName.size()-1] );
   for (d = readdir(dir); d; d = readdir(dir))
     {
     fileName = dirName + d->d_name;
@@ -152,7 +152,7 @@ unsigned int Directory::Explore(FilenameType const &name, bool recursive)
         || strcmp( d->d_name, ".." ) == 0
         || d->d_name[0] == '.' ) // discard any hidden dir
         continue;
-      assert( d->d_name[0] != '.' ); // hidden directory ??
+      gdcm_assert( d->d_name[0] != '.' ); // hidden directory ??
       if ( recursive )
         {
         nFiles += Explore( fileName, recursive);

Modules/ThirdParty/GDCM/src/gdcm/Source/Common/gdcmDirectory.h

@@ -56,7 +56,7 @@ public :
 
   /// Set/Get the file names within the directory
   FilenamesType const &GetFilenames() const {
-    assert( !(Toplevel.empty()) && "Need to call Explore first" );
+    gdcm_assert( !(Toplevel.empty()) && "Need to call Explore first" );
     return Filenames; }
 
   /// Return the Directories traversed

Modules/ThirdParty/GDCM/src/gdcm/Source/Common/gdcmException.h

@@ -31,6 +31,8 @@
 # endif
 #endif
 
+#define gdcm_forced_assert(cond) assert(cond)
+
 namespace gdcm
 {
 
@@ -54,9 +56,9 @@ class Exception : public std::exception
                                  const unsigned int lineNumber,
                                  const char* const func)
   {
-    assert(desc != nullptr);
-    assert(file != nullptr);
-    assert(func != nullptr);
+    gdcm_forced_assert(desc != nullptr);
+    gdcm_forced_assert(file != nullptr);
+    gdcm_forced_assert(func != nullptr);
     std::ostringstream oswhat;
     oswhat << file << ":" << lineNumber << " (" << func << "):\n";
     oswhat << desc;
@@ -98,6 +100,17 @@ class Exception : public std::exception
 
 } // end namespace gdcm
 
+// Always defined
+#define gdcm_assert(cond) \
+  if (!(cond)) throw gdcm::Exception("An invalid logic behavior occurred" #cond, __FILE__ , __LINE__)
+
+/* Asserts that should only exist in debug builds. */
+#ifndef NDEBUG // checks in debug builds and elision in release builds (like assert)
+#define gdcm_debug_assert(cond) gdcm_assert(cond)
+#else
+#define gdcm_debug_assert(cond) ((void)0)
+#endif
+
 // Undo warning suppression.
 #if defined(__clang__) && defined(__has_warning)
 # if __has_warning("-Wdeprecated")

Modules/ThirdParty/GDCM/src/gdcm/Source/Common/gdcmFilename.cxx

@@ -17,6 +17,10 @@
 #include <cstdlib> // realpath
 #include <cstring>
 
+#if defined(_WIN32) && (defined(_MSC_VER) || defined(__WATCOMC__) || defined(__BORLANDC__) || defined(__MINGW32__))
+#include <windows.h>
+#endif
+
 namespace gdcm
 {
 
@@ -48,7 +52,7 @@ const char *Filename::GetPath()
 const char *Filename::GetName()
 {
   std::string filename = FileName;
-  assert( !filename.empty() );
+  gdcm_assert( !filename.empty() );
 #if defined(_WIN32)
   std::string::size_type slash_pos = filename.find_last_of("/\\");
 #else
@@ -65,7 +69,7 @@ const char *Filename::GetName()
 const char *Filename::ToWindowsSlashes()
 {
   Conversion = FileName;
-  //assert( !Conversion.empty() );
+  //gdcm_assert( !Conversion.empty() );
   for (std::string::iterator it = Conversion.begin(); it != Conversion.end(); ++it )
     {
     if( *it == '/' )
@@ -82,13 +86,13 @@ const char *Filename::ToUnixSlashes()
 {
   Conversion = FileName;
   //std::string::size_type s = Conversion.find("\\");
-  //assert( s == std::string::npos );
-  assert( !Conversion.empty() );
+  //gdcm_assert( s == std::string::npos );
+  gdcm_assert( !Conversion.empty() );
   for (std::string::iterator it = Conversion.begin(); it != Conversion.end(); ++it )
     {
     if( *it == '\\' )
       {
-      assert( it+1 == Conversion.end() || *(it+1) != ' ' ); // is it an escaped space ?
+      gdcm_assert( it+1 == Conversion.end() || *(it+1) != ' ' ); // is it an escaped space ?
       *it = '/';
       }
     }
@@ -97,7 +101,6 @@ const char *Filename::ToUnixSlashes()
 }
 
 #if defined(_WIN32) && (defined(_MSC_VER) || defined(__WATCOMC__) || defined(__BORLANDC__) || defined(__MINGW32__))
-#include <windows.h>
 
 inline void Realpath(const char *path, std::string & resolved_path)
 {