ITK5 migration

Superbuild/ITKExternal.cmake

@@ -50,7 +50,9 @@ SET(itk_CACHE_ARGS
   "-DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}"
   "-DCMAKE_INSTALL_PREFIX:PATH=<INSTALL_DIR>"
   "-DITK_BUILD_DEFAULT_MODULES:BOOL=OFF"
-  "-DITKV3_COMPATIBILITY:BOOL=ON"
+  "-DITKV4_COMPATIBILITY:BOOL=OFF"
+  "-DITK_LEGACY_REMOVE:BOOL=ON"
+  "-DITK_FUTURE_LEGACY_REMOVE:BOOL=OFF"
   "-DModule_ITKRegistrationCommon:BOOL=ON"
   "-DModule_ITKSmoothing:BOOL=ON"
   "-DModule_ITKAnisotropicSmoothing:BOOL=ON"
@@ -68,7 +70,7 @@ SET(itk_CACHE_ARGS
   "-DModule_ITKIOGIPL:BOOL=ON"
   "-DModule_IITKIOMeta:BOOL=ON"
   "-DModule_ITKIONRRD:BOOL=ON"
-  "-DModule_ITKDeprecated:BOOL=ON"
+  "-DModule_ITKDeprecated:BOOL=OFF"
   "-DCMAKE_CXX_FLAGS:STATIC=${CMAKE_CXX_FLAGS}"
   "-DCMAKE_CXX_FLAGS_DEBUG:STATIC=${CMAKE_CXX_FLAGS_DEBUG}"
   "-DCMAKE_C_FLAGS:STATIC=${CMAKE_C_FLAGS}"
@@ -86,12 +88,12 @@ IF(BUILD_MOSAIC_TOOLS)
   )
 ENDIF()
 
-SET(itk_GIT_TAG "origin/itk-4.13.1")
+SET(itk_GIT_TAG "master")
 
 # If CMake ever allows overriding the checkout command or adding flags,
 # git checkout -q will silence message about detached head (harmless).
 ExternalProject_Add(ITK_external
-  GIT_REPOSITORY "https://github.com/CIBC-Internal/itk.git"
+  GIT_REPOSITORY "https://github.com/InsightSoftwareConsortium/ITK.git"
   GIT_TAG ${itk_GIT_TAG}
   UPDATE_COMMAND ""
   PATCH_COMMAND ""
@@ -101,6 +103,6 @@ ExternalProject_Add(ITK_external
 
 # hardcoded, since we need this before ITK's configure step
 ExternalProject_Get_Property(ITK_external INSTALL_DIR)
-SET(ITK_DIR "${INSTALL_DIR}/lib/cmake/ITK-4.13" CACHE PATH "")
+SET(ITK_DIR "${INSTALL_DIR}/lib/cmake/ITK-5.2" CACHE PATH "")
 
 MESSAGE(STATUS "ITK_DIR=${ITK_DIR}")

Superbuild/Superbuild.cmake

@@ -156,22 +156,16 @@ ENDIF()
 IF(SEG3D_BUILD_INTERFACE)
   SET(Qt5_PATH "" CACHE PATH "Path to directory where Qt 5 is installed. Directory should contain lib and bin subdirectories.")
   #SET(CMAKE_AUTOMOC ON)
+
+  FIND_PACKAGE(Qt5 COMPONENTS Core Gui OpenGL Svg REQUIRED HINTS ${Qt5_PATH})
 
-  IF(IS_DIRECTORY ${Qt5_PATH})
-    FIND_PACKAGE(Qt5Core REQUIRED HINTS ${Qt5_PATH})
-    FIND_PACKAGE(Qt5Gui REQUIRED HINTS ${Qt5_PATH})
-    FIND_PACKAGE(Qt5OpenGL REQUIRED HINTS ${Qt5_PATH})
-  ELSE()
-    MESSAGE(SEND_ERROR "Set Qt5_PATH to directory where Qt 5 is installed (containing lib and bin subdirectories) or set SEG3D_BUILD_INTERFACE to OFF.")
-  ENDIF()
-
-  IF(Qt5Core_FOUND)
-    MESSAGE(STATUS "Found Qt version: ${Qt5Core_VERSION}")
-    IF(${Qt5Core_VERSION} VERSION_LESS "5.12")
+  IF(Qt5_FOUND)
+    MESSAGE(STATUS "Found Qt version: ${Qt5_VERSION}")
+    IF(${Qt5_VERSION} VERSION_LESS "5.12")
       MESSAGE(FATAL_ERROR "Qt 5.12 or greater is required for building the Seg3D GUI")
     ENDIF()
   ELSE()
-    MESSAGE(FATAL_ERROR "Qt5 is required for building the Seg3D GUI")
+    MESSAGE(FATAL_ERROR "Qt5 is required for building the Seg3D GUI. Set Qt5_PATH to directory where Qt 5 is installed (containing lib and bin subdirectories) or set SEG3D_BUILD_INTERFACE to OFF.")
   ENDIF()
 
   IF(APPLE)
@@ -343,6 +337,7 @@ IF(SEG3D_BUILD_INTERFACE)
     "-DQt5Core_DIR:PATH=${Qt5Core_DIR}"
     "-DQt5Gui_DIR:PATH=${Qt5Gui_DIR}"
     "-DQt5OpenGL_DIR:PATH=${Qt5OpenGL_DIR}"
+    "-DQt5Svg_DIR:PATH=${Qt5Svg_DIR}"
     "-DMACDEPLOYQT_OUTPUT_LEVEL:STRING=${MACDEPLOYQT_OUTPUT_LEVEL}"
   )
 ENDIF()

src/Application/Clipboard/ClipboardItem.cc

@@ -68,7 +68,7 @@ ClipboardItem::~ClipboardItem()
 
 ClipboardItemHandle ClipboardItem::clone() const
 {
-  ClipboardItem* cpy = new ClipboardItem( this->private_->width_, 
+  ClipboardItem* cpy = new ClipboardItem( this->private_->width_,
     this->private_->height_, this->private_->data_type_ );
   cpy->private_->buffer_ = this->private_->buffer_;
   cpy->private_->provenance_id_ = this->private_->provenance_id_;
@@ -126,6 +126,10 @@ void ClipboardItem::resize( size_t width, size_t height, Core::DataType data_typ
   case Core::DataType::UINT_E:
     buffer_size = sizeof( int );
     break;
+  case Core::DataType::LONGLONG_E:
+  case Core::DataType::ULONGLONG_E:
+    buffer_size = sizeof( long long );
+    break;
   case Core::DataType::FLOAT_E:
     buffer_size = sizeof( float );
     break;

src/Application/DatabaseManager/DatabaseManager.cc

@@ -80,7 +80,7 @@ DatabaseManager::DatabaseManager( const DatabaseManager& src ) :
       "main", src.private_->database_, "main" );
     if ( db_backup_obj == NULL )
     {
-      CORE_THROW_EXCEPTION( std::string( "Failed to copy database: " ) + 
+      CORE_THROW_EXCEPTION( std::string( "Failed to copy database: " ) +
         sqlite3_errmsg( this->private_->database_ ) );
     }
 
@@ -94,7 +94,7 @@ DatabaseManager::DatabaseManager( const DatabaseManager& src ) :
 }
 
 DatabaseManager::~DatabaseManager()
-{ 
+{
   // We need to close the database to avoid memory leak.
   if ( this->private_->database_ )
   {
@@ -118,7 +118,7 @@ static int InternalExecuteSqlStatement( sqlite3_stmt* statement, ResultSet& resu
       case SQLITE_TEXT:
       case SQLITE_BLOB:
         {
-          std::string string_result = std::string( reinterpret_cast< const char* >( 
+          std::string string_result = std::string( reinterpret_cast< const char* >(
             sqlite3_column_text( statement, j ) ) );
           temp_any = boost::any( string_result );
           break;
@@ -156,7 +156,7 @@ bool DatabaseManager::run_sql_statement( const std::string& sql_str, std::string
   return this->run_sql_statement( sql_str, dummy_results, error );
 }
 
-bool DatabaseManager::run_sql_statement( const std::string& sql_str, ResultSet& results, 
+bool DatabaseManager::run_sql_statement( const std::string& sql_str, ResultSet& results,
   std::string& error )
 {
   results.clear();
@@ -170,7 +170,7 @@ bool DatabaseManager::run_sql_statement( const std::string& sql_str, ResultSet&
   }
 
   sqlite3_stmt* statement = NULL;
-  if ( sqlite3_prepare_v2( this->private_->database_, sql_str.c_str(), 
+  if ( sqlite3_prepare_v2( this->private_->database_, sql_str.c_str(),
     static_cast< int >( sql_str.size() ), &statement, NULL ) != SQLITE_OK )
   {
     error =  "The SQL statement '" + sql_str + "' failed to compile with error: "
@@ -183,7 +183,7 @@ bool DatabaseManager::run_sql_statement( const std::string& sql_str, ResultSet&
     error =  "The SQL statement '" + sql_str + "' returned error: "
       + sqlite3_errmsg( this->private_->database_ );
     return false;
-  } 
+  }
 
   return true;
 }
@@ -202,11 +202,11 @@ bool DatabaseManager::run_sql_script( const std::string& sql_str, std::string& e
   const char* head = sql_str.c_str();
   const char* tail = NULL;
   // The input string length including the null terminator
-  int num_bytes = static_cast< int >( sql_str.size() + 1 ); 
+  int num_bytes = static_cast< int >( sql_str.size() + 1 );
   while ( num_bytes > 1 )
   {
     sqlite3_stmt* statement = NULL;
-    if ( sqlite3_prepare_v2( this->private_->database_, head, 
+    if ( sqlite3_prepare_v2( this->private_->database_, head,
       num_bytes, &statement, &tail ) != SQLITE_OK )
     {
       error =  "The SQL statement '" + std::string( head ) + "' failed to compile with error: "
@@ -221,7 +221,7 @@ bool DatabaseManager::run_sql_script( const std::string& sql_str, std::string& e
       error =  "The SQL statement '" + std::string( head ) + "' returned error: "
         + sqlite3_errmsg( this->private_->database_ );
       return false;
-    } 
+    }
 
     num_bytes -= static_cast< int >( tail - head );
     head = tail;
@@ -230,87 +230,87 @@ bool DatabaseManager::run_sql_script( const std::string& sql_str, std::string& e
   return true;
 }
 
-bool DatabaseManager::load_database( const boost::filesystem::path& database_file, 
+bool DatabaseManager::load_database( const boost::filesystem::path& database_file,
   std::string& error )
 {
   DatabaseManagerPrivate::lock_type lock( this->private_->get_mutex() );
 
   int result;
   sqlite3* temp_open_database;
   sqlite3_backup* backup_database_object;
-  
+
   result = sqlite3_open( database_file.string().c_str(), &temp_open_database );
-  
-  if ( result != SQLITE_OK ) 
+
+  if ( result != SQLITE_OK )
   {
     sqlite3_close( temp_open_database );
     error = std::string( "Could not open database file '" ) + database_file.string() + "'.";
     return false;
   }
-  
-  backup_database_object = 
+
+  backup_database_object =
     sqlite3_backup_init( this->private_->database_, "main", temp_open_database, "main" );
-  
+
   if ( backup_database_object )
   {
     sqlite3_backup_step( backup_database_object, -1 );
     sqlite3_backup_finish( backup_database_object );
   }
-  
+
   sqlite3_close( temp_open_database );
 
   result = sqlite3_errcode( this->private_->database_ );
-  if ( result != SQLITE_OK ) 
+  if ( result != SQLITE_OK )
   {
     error = "Internal error in database.";
     return false;
   }
-  
+
   // Enable foreign key
   this->run_sql_statement( "PRAGMA foreign_keys = ON;", error );
 
   error = "";
-  return true;  
+  return true;
 }
 
 
-bool DatabaseManager::save_database( const boost::filesystem::path& database_file, 
+bool DatabaseManager::save_database( const boost::filesystem::path& database_file,
   std::string& error )
 {
   DatabaseManagerPrivate::lock_type lock( this->private_->get_mutex() );
   int result;
   sqlite3* temp_open_database;
   sqlite3_backup* backup_database_object;
-  
+
   result = sqlite3_open( database_file.string().c_str(), &temp_open_database );
-  
-  if ( result != SQLITE_OK ) 
+
+  if ( result != SQLITE_OK )
   {
     sqlite3_close( temp_open_database );
     error = std::string( "Could not open database file '" ) + database_file.string() + "'.";
     return false;
   }
-  
-  backup_database_object = 
+
+  backup_database_object =
     sqlite3_backup_init( temp_open_database, "main", this->private_->database_, "main" );
-  
+
   if ( backup_database_object )
   {
     sqlite3_backup_step( backup_database_object, -1 );
     sqlite3_backup_finish( backup_database_object );
   }
-  
+
   result = sqlite3_errcode( temp_open_database );
-  if ( result != SQLITE_OK ) 
+  if ( result != SQLITE_OK )
   {
     error = "Internal error in database.";
     return false;
   }
-  
+
   sqlite3_close( temp_open_database );
 
   error = "";
-  return true;  
+  return true;
 }
 
 long long DatabaseManager::get_last_insert_rowid()
@@ -323,9 +323,9 @@ long long DatabaseManager::get_last_insert_rowid()
   return 0;
 }
 
-bool DatabaseManager::get_column_metadata( const std::string& table_name, 
-                      const std::string& column_name, char const** data_type /*= NULL*/, 
-                      char const** coll_seq /*= NULL*/, int* not_null /*= NULL*/, 
+bool DatabaseManager::get_column_metadata( const std::string& table_name,
+                      const std::string& column_name, char const** data_type /*= NULL*/,
+                      char const** coll_seq /*= NULL*/, int* not_null /*= NULL*/,
                       int* primary_key /*= NULL*/, int* auto_inc /*= NULL */ )
 {
   if ( this->private_->database_ == 0 )

src/Application/DatabaseManager/DatabaseManager.h

@@ -31,7 +31,7 @@
 
 #if defined(_MSC_VER) && (_MSC_VER >= 1020)
 # pragma once
-#endif 
+#endif
 
 // STL includes
 #include <map>
@@ -64,7 +64,7 @@ class DatabaseManager : public boost::noncopyable
   DatabaseManager( const DatabaseManager& src );
 
   virtual ~DatabaseManager();
-  
+
 public:
   /// RUN_SQL_STATEMENT:
   /// Execute the given SQL statement on the database. If the statement generates
@@ -76,15 +76,15 @@ class DatabaseManager : public boost::noncopyable
   /// Execute the given SQL statement on the database.
   /// Returns true on success, otherwise false.
   bool run_sql_statement( const std::string& sql_str, std::string& error );
-  
+
   /// RUN_SQL_SCRIPT:
   /// Execute multiple SQL statements sequentially.
   bool run_sql_script( const std::string& sql_str, std::string& error );
 
   /// SAVE_DATABASE:
   /// Save the database to disk
   bool save_database( const boost::filesystem::path& database_file, std::string& error );
-  
+
   /// LOAD_DATABASE:
   /// Load the database from disk
   bool load_database( const boost::filesystem::path& database_file, std::string& error );
@@ -97,8 +97,8 @@ class DatabaseManager : public boost::noncopyable
   /// Get metadata about a specific column of a specific database table.
   /// Returns true if the table and column exist, otherwise false.
   bool get_column_metadata( const std::string& table_name, const std::string& column_name,
-    char const** data_type = NULL, char const** coll_seq = NULL, 
-    int* not_null = NULL, int* primary_key = NULL, int* auto_inc = NULL ); 
+    char const** data_type = NULL, char const** coll_seq = NULL,
+    int* not_null = NULL, int* primary_key = NULL, int* auto_inc = NULL );
 
 private:
   boost::shared_ptr< DatabaseManagerPrivate > private_;
@@ -112,4 +112,3 @@ class DatabaseManager : public boost::noncopyable
 } // end namespace seg3d
 
 #endif
-