[MERGE] with af067365b90d687a0fc85d93bc734d35edeee81d

doc/user/walnut.cfg.mpi

@@ -12,7 +12,7 @@ allowOnlyOneFiberDataSet = yes # This will prevent you from accidently loading m
 # default=HUD
 ## A list of modules that will be provided through the GUI. 
 ## If the list is empty all available modules are provided.
-whiteList = Arbitrary Plane,Coordinate System,Image Extractor,Paint Texture,Arbitrary Rois,Bounding Box,Distance Map Isosurface,Gauss Filtering,HUD,Isosurface,Isosurface Raytracer,LIC,Mesh Reader,Voxelizer,Superquadric Glyphs,Triangle Mesh Renderer,Vector Plot,Write NIfTI
+whiteList = Arbitrary Plane,Coordinate System,Image Extractor,Paint Texture,Arbitrary Rois,Bounding Box,Distance Map Isosurface,Gauss Filtering,HUD,Isosurface,Isosurface Raytracer,LIC,Read Mesh,Voxelizer,Superquadric Glyphs,Triangle Mesh Renderer,Vector Plot,Write NIfTI
 
 ## Specify a ";" separated list of additional paths for modules. The order of appearance is the order of loading. The following additional rules apply here:
 ## 1. if the directory contains one or more libOWmodule_XYZ it/they get loaded

src/CMakeLists.txt

@@ -152,6 +152,8 @@ IF( CMAKE_GENERATOR MATCHES "Visual Studio" )
     SET( CMAKE_SHARED_LINKER_FLAGS " /STACK:10000000 /machine:I386 /NODEFAULTLIB:${EXCLUDE_LIBRARIES}"  CACHE STRING "" FORCE )
     SET( CMAKE_EXE_LINKER_FLAGS " /STACK:10000000 /machine:I386 /NODEFAULTLIB:${EXCLUDE_LIBRARIES}"  CACHE STRING "" FORCE )
     SET( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /D \"NOMINMAX\"" )
+    SET( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /MP" )
+	SET( CMAKE_DEBUG_POSTFIX "d" CACHE STRING "add a postfix, usually d on windows" )
 ELSE()
     # Unfortunately libstdc++'s header files don't work with mingw in ansi mode (basically libstdc++'s fault)
     IF( CMAKE_HOST_SYSTEM MATCHES "Windows" )
@@ -208,6 +210,11 @@ ENDIF()
 ADD_EXECUTABLE( walnut OpenWalnut.cpp version.h )
 TARGET_LINK_LIBRARIES( walnut OWkernel OWdataHandler OWgui OWguiqt4 OWcommon OWge ${Boost_LIBRARIES} )
 
+IF(MSVC_IDE)
+	SET_TARGET_PROPERTIES( walnut PROPERTIES DEBUG_POSTFIX "d")
+	SET_TARGET_PROPERTIES( walnut PROPERTIES PREFIX "../")    
+ENDIF(MSVC_IDE)
+
 #---------- Shaders -------------
 option( OW_COPY_SHADERS "This enables copying shaders with every make call." ON )
 if( OW_COPY_SHADERS )

src/common/CMakeLists.txt

@@ -10,6 +10,10 @@ ADD_SUBDIRECTORY( math )
 ADD_LIBRARY( OWcommon SHARED ${COMMON_SRC} ${COMMON_DATASTRUCTURES_SRC} ${COMMON_EXCEPTIONS_SRC} ${MATH_SRC} ${FIBERSIMILARITY_SRC} )
 TARGET_LINK_LIBRARIES( OWcommon ${Boost_LIBRARIES} ${CMAKE_DL_LIBS} )
 
+IF(MSVC_IDE)
+	SET_TARGET_PROPERTIES( OWcommon PROPERTIES PREFIX "../")    
+ENDIF(MSVC_IDE)
+
 # Set the prefix and suffix of dynamically loadable modules to match
 # CMAKEs naming of them. The quotes are necessary so the shell doesn't mess
 # with these defines. Unfortunately, the Visual Studio has problems handling

src/common/WPathHelper.cpp

@@ -24,6 +24,7 @@
 
 #include <string>
 #include <vector>
+#include <cstdlib>
 
 #include <boost/tokenizer.hpp>
 
@@ -70,7 +71,22 @@ boost::filesystem::path WPathHelper::getAppPath()
 boost::filesystem::path WPathHelper::getConfigFile()
 {
     // TODO(ebaum): we should prefer a user config file in ~.walnut.cfg in future. This needs to be platform independent of course.
-    return getPathHelper()->m_sharePath / "walnut.cfg";
+    namespace fs = boost::filesystem;
+
+    // I know that this work only for linux, but it should not break anything elsewhere.
+    // Thus, we prefer the file in the home directory now.
+    std::string homeDir = getenv( "HOME" ) ? getenv( "HOME" ) : "";
+    std::string linuxDefault= homeDir + "/.walnut.cfg";
+    boost::filesystem::path configFile;
+    if( fs::exists( linuxDefault ) )
+    {
+        configFile = boost::filesystem::path( linuxDefault );
+    }
+    else
+    {
+        configFile = getPathHelper()->m_sharePath / "walnut.cfg";
+    }
+    return configFile;
 }
 
 boost::filesystem::path WPathHelper::getFontPath()

src/common/WPathHelper.h

@@ -39,11 +39,6 @@ class OWCOMMON_EXPORT WPathHelper // NOLINT
 {
 public:
 
-    /**
-     * Default constructor.
-     */
-    WPathHelper();
-
     /**
      * Destructor.
      */
@@ -157,6 +152,11 @@ public:
 
 protected:
 
+    /**
+     * Constructors are protected because this is a Singleton.
+     */
+    WPathHelper();
+
 private:
 
     /**

src/dataHandler/CMakeLists.txt

@@ -24,6 +24,11 @@ FILE( GLOB DATAHANDLER_IO_SRC "io/*.cpp" "io/*.h" ) # former WLoader
         TARGET_LINK_LIBRARIES( OWdataHandler OWcommon ${Boost_LIBRARIES} OWext_niftiio OWext_biosig OWext_eep ${OPENSCENEGRAPH_LIBRARIES} )
     ENDIF()
 #ENDIF()
+
+IF(MSVC_IDE)
+	SET_TARGET_PROPERTIES( OWdataHandler PROPERTIES PREFIX "../")    
+ENDIF(MSVC_IDE)
+
 # Unit tests
 IF( OW_COMPILE_TESTS )
     # in case of not installed ITK the unit test won't compile, so we remove it

src/ext/libeep/CMakeLists.txt

@@ -16,3 +16,7 @@ IF( CMAKE_GENERATOR MATCHES "Visual Studio" )
 ELSE()
 	TARGET_LINK_LIBRARIES( OWext_eep m )
 ENDIF()
+
+IF(MSVC_IDE)
+	SET_TARGET_PROPERTIES( OWext_eep PROPERTIES PREFIX "../")    
+ENDIF(MSVC_IDE)

src/ext/nifti/CMakeLists.txt

@@ -42,6 +42,9 @@ SET(NIFTI_NIFTILIB_NAME ${PACKAGE_PREFIX}niftiio)
 ADD_LIBRARY(${NIFTI_NIFTILIB_NAME} ${NIFTILIB_SRC} )
 TARGET_LINK_LIBRARIES( ${NIFTI_NIFTILIB_NAME} ${PACKAGE_PREFIX}znz)
 
+IF(MSVC_IDE)
+	SET_TARGET_PROPERTIES( ${NIFTI_NIFTILIB_NAME} PROPERTIES PREFIX "../")    
+ENDIF(MSVC_IDE)
 
 IF(UNIX)
   TARGET_LINK_LIBRARIES(${NIFTI_NIFTILIB_NAME} -lm)

src/graphicsEngine/CMakeLists.txt

@@ -10,6 +10,10 @@ FILE( GLOB GE_SRC "*.cpp" "*.h" )
 ADD_LIBRARY( OWge SHARED ${GE_SRC} ${GE_EXCEPTIONS_SRC} ${GE_CALLBACKS_SRC} ${GE_ALGORITHMS_SRC} )
 TARGET_LINK_LIBRARIES( OWge OWcommon ${OPENGL_gl_LIBRARY} ${OPENSCENEGRAPH_LIBRARIES} )
 
+IF(MSVC_IDE)
+	SET_TARGET_PROPERTIES( OWge PROPERTIES PREFIX "../")    
+ENDIF(MSVC_IDE)
+
 # Unit tests
 IF( OW_COMPILE_TESTS )
   CXXTEST_ADD_TESTS_FROM_LIST( "${GE_SRC}" "OWge;OWkernel"

src/graphicsEngine/WGEUtils.h

@@ -88,12 +88,6 @@ namespace wge
      */
     osg::Vec3 WGE_EXPORT unprojectFromScreen( const osg::Vec3 screen, osg::ref_ptr< osg::Camera > camera  );
 
-    /**
-     * Conversion of WVector3D to osg::Vec3
-     * \param v the vector to convert.
-     */
-    osg::Vec3 wv3D2ov3( wmath::WVector3D v );
-
     /**
      * creates the same color as the atlas colormap shader from the index
      *
@@ -180,11 +174,6 @@ inline osg::Vec3 wge::osgVec3( const wmath::WPosition& pos )
     return osg::Vec3( pos[0], pos[1], pos[2] );
 }
 
-inline osg::Vec3 wge::wv3D2ov3( wmath::WVector3D v )
-{
-    return osg::Vec3( v[0], v[1], v[2] );
-}
-
 inline osg::Matrixd wge::toOSGMatrix( const wmath::WMatrix<double>& matrix )
 {
     WAssert( ( matrix.getNbRows() == 3 || matrix.getNbRows() == 4 ) && ( matrix.getNbCols() == 3 || matrix.getNbCols() == 4 ),

src/graphicsEngine/WGraphicsEngine.h

@@ -62,11 +62,6 @@ class WGE_EXPORT WGraphicsEngine: public WThreadedRunner
 {
 public:
 
-    /**
-     * Default constructor.
-     */
-    explicit WGraphicsEngine();
-
     /**
      * Destructor.
      */
@@ -142,6 +137,11 @@ public:
 
 protected:
 
+    /**
+     * Constructors are protected because this is a Singleton.
+     */
+    explicit WGraphicsEngine();
+
     /**
      * Handler for repainting and event handling. Gets executed in separate thread.
      */

src/gui/CMakeLists.txt

@@ -5,6 +5,10 @@ FILE( GLOB GUI_SRC "*.cpp" "*.h" )
 ADD_LIBRARY( OWgui ${GUI_SRC} )
 TARGET_LINK_LIBRARIES( OWgui OWcommon )
 
+IF(MSVC_IDE)
+	SET_TARGET_PROPERTIES( OWgui PROPERTIES PREFIX "../")    
+ENDIF(MSVC_IDE)
+
 # Unit tests
 IF( OW_COMPILE_TESTS )
   CXXTEST_ADD_TESTS_FROM_LIST( "${GUI_SRC}"

src/gui/qt4/CMakeLists.txt

@@ -41,3 +41,7 @@ FILE(GLOB GUI_QT4_SRC "*.cpp" "guiElements/*.cpp" "controlPanel/*.cpp" "ribbonMe
 
 ADD_LIBRARY( OWguiqt4 ${GUI_QT4_SRC} ${GUI_QT4_MOC_SRCS} )
 TARGET_LINK_LIBRARIES( OWguiqt4 OWcommon OWgui OWge OWkernel ${QT_LIBS} ${Boost_LIBRARIES} )
+
+IF(MSVC_IDE)
+	SET_TARGET_PROPERTIES( OWguiqt4 PROPERTIES PREFIX "../")    
+ENDIF(MSVC_IDE)

src/gui/qt4/WQt4Gui.cpp

@@ -150,7 +150,7 @@ int WQt4Gui::run()
     m_ge = WGraphicsEngine::getGraphicsEngine();
 
     // and startup kernel
-    m_kernel = boost::shared_ptr< WKernel >( new WKernel( m_ge, shared_from_this() ) );
+    m_kernel = boost::shared_ptr< WKernel >( WKernel::instance( m_ge, shared_from_this() ) );
     m_kernel->run();
     t_ModuleErrorSignalHandlerType func = boost::bind( &WQt4Gui::moduleError, this, _1, _2 );
     m_kernel->getRootContainer()->addDefaultNotifier( WM_ERROR, func );

src/kernel/CMakeLists.txt

@@ -8,6 +8,10 @@ FILE( GLOB KERNEL_COMBINER_SRC "combiner/*.cpp" "combiner/*.h" )
 ADD_LIBRARY( OWkernel SHARED ${KERNEL_SRC} ${MODULES_SRC} ${KERNEL_EXCEPTIONS_SRC} ${KERNEL_COMBINER_SRC} )
 TARGET_LINK_LIBRARIES( OWkernel OWcommon OWdataHandler OWge ${OPENSCENEGRAPH_LIBRARIES} ${CMAKE_DL_LIBS} )
 
+IF(MSVC_IDE)
+	SET_TARGET_PROPERTIES( OWkernel PROPERTIES PREFIX "../")    
+ENDIF(MSVC_IDE)
+
 # Unit tests
 IF( OW_COMPILE_TESTS )
     #    SET( testLibs guiqt4 )

src/kernel/WKernel.cpp

@@ -50,7 +50,7 @@
 /**
  * Used for program wide access to the kernel.
  */
-WKernel* kernel = NULL;
+WKernel* WKernel::m_kernel = NULL;
 
 WKernel::WKernel( boost::shared_ptr< WGraphicsEngine > ge, boost::shared_ptr< WGUI > gui ):
     WThreadedRunner()
@@ -58,7 +58,7 @@ WKernel::WKernel( boost::shared_ptr< WGraphicsEngine > ge, boost::shared_ptr< WG
     WLogger::getLogger()->addLogMessage( "Initializing Kernel", "Kernel", LL_INFO );
 
     // init the singleton
-    kernel = this;
+    m_kernel = this;
 
     // initialize members
     m_gui = gui;
@@ -74,6 +74,16 @@ WKernel::~WKernel()
     WLogger::getLogger()->addLogMessage( "Shutting down Kernel", "Kernel", LL_INFO );
 }
 
+WKernel* WKernel::instance( boost::shared_ptr< WGraphicsEngine > ge, boost::shared_ptr< WGUI > gui )
+{
+    if( m_kernel == NULL )
+    {
+        new WKernel( ge, gui ); // m_kernel will be set in the constructor.
+    }
+
+    return m_kernel;
+}
+
 void WKernel::init()
 {
     // initialize
@@ -99,7 +109,7 @@ void WKernel::init()
 
 WKernel* WKernel::getRunningKernel()
 {
-    return kernel;
+    return m_kernel;
 }
 
 boost::shared_ptr< WGraphicsEngine > WKernel::getGraphicsEngine() const

src/kernel/WKernel.h

@@ -64,12 +64,15 @@ class OWKERNEL_EXPORT WKernel: public WThreadedRunner
 public:
 
     /**
-     * Constructor. Awaits an INITIALIZED graphics engine an gui.
+     * Returns pointer to the running kernel or a new if no kernel was there.
+     * If a running kernel exists the function return it and does not check if
+     * ge and gui of the running kernel are equivalent to the ones given as parameters.
      *
      * \param ge initialized graphics engine.
      * \param gui initialized gui.
+     * \return the kernel instance.
      */
-    WKernel( boost::shared_ptr< WGraphicsEngine > ge, boost::shared_ptr< WGUI > gui );
+    static WKernel* instance( boost::shared_ptr< WGraphicsEngine > ge, boost::shared_ptr< WGUI > gui );
 
     /**
      * Destructor.
@@ -155,6 +158,14 @@ public:
     boost::shared_ptr< WSelectionManager>getSelectionManager();
 
 protected:
+    /**
+     * Constructor is protected because this class is a singleton. Awaits an INITIALIZED graphics engine an gui.
+     *
+     * \param ge initialized graphics engine.
+     * \param gui initialized gui.
+     */
+    WKernel( boost::shared_ptr< WGraphicsEngine > ge, boost::shared_ptr< WGUI > gui );
+
 
     /**
      * Function that has to be overwritten for execution. It gets executed in a separate thread after run()
@@ -202,6 +213,11 @@ private:
      * Initializes the graphics engine, data handler and so on.
      */
     void init();
+
+    /**
+     * Pointer to the unique instance of this singleton class.
+     */
+    static WKernel* m_kernel;
 };
 
 #endif  // WKERNEL_H

src/kernel/WModuleFactory.h

@@ -72,11 +72,6 @@ public:
      */
     typedef WSharedAssociativeContainer< PrototypeContainerType > PrototypeSharedContainerType;
 
-    /**
-     * Default constructor.
-     */
-    WModuleFactory();
-
     /**
      * Destructor.
      */
@@ -182,6 +177,10 @@ public:
     static bool isPrototype( boost::shared_ptr< WModule > module );
 
 protected:
+    /**
+     * Constructors are protected because this is a Singleton.
+     */
+    WModuleFactory();
 
     /**
      * The module prototypes available.

src/kernel/WModuleLoader.cpp

@@ -56,8 +56,21 @@ void WModuleLoader::load( WSharedAssociativeContainer< std::set< boost::shared_p
         std::string suffix = wiotools::getSuffix( i->leaf() );
         std::string stem = i->path().stem();
 
+#ifdef _MSC_VER
+        std::string supposedFilename = getModulePrefix() + '_' + i->path().parent_path().filename()
+#ifdef _DEBUG
+            + 'd'
+#endif
+            + WSharedLib::getSystemSuffix();
+        std::string isFileName = i->path().filename();
+#endif // _MSC_VER
+
         if( !boost::filesystem::is_directory( *i ) && ( suffix == WSharedLib::getSystemSuffix() ) &&
-            ( stem.compare( 0, getModulePrefix().length(), getModulePrefix() ) == 0 ) )
+            ( stem.compare( 0, getModulePrefix().length(), getModulePrefix() ) == 0 )
+#ifdef _MSC_VER
+            && supposedFilename == isFileName
+#endif
+            )
         {
             try
             {
@@ -104,19 +117,6 @@ void WModuleLoader::load( WSharedAssociativeContainer< std::set< boost::shared_p
             // if it a dir -> traverse down
             load( ticket, *i, level + 1 );
         }
-        // this little construct will enable vc to find the dll's in the correct build mode we are in
-#ifdef _MSC_VER
-        else if ( ( level == 1 ) &&
-#ifdef _DEBUG
-            boost::filesystem::path( *i ).filename() == "Debug"
-#else // _DEBUG
-            boost::filesystem::path( *i ).filename() == "Release"
-#endif // _DEBUG
-            )
-        {
-            load( ticket, *i, level + 1 );
-        }
-#endif // _MSC_VER
     }
 }
 

src/kernel/modules/navSlices/WMNavSlices.cpp

@@ -510,7 +510,7 @@ void WMNavSlices::setSlicePosFromPick( WPickInfo pickInfo )
             osg::Vec3 endPosWorld = wge::unprojectFromScreen( endPosScreen, m_viewer->getCamera() );
 
             osg::Vec3 moveDirWorld = endPosWorld - startPosWorld;
-            float diff = wge::wv3D2ov3( normal ) * moveDirWorld;
+            float diff = normal * moveDirWorld;
 
             // recognize also small values.
             if( diff < 0 && diff > -1 )
@@ -628,7 +628,7 @@ osg::ref_ptr<osg::Geometry> WMNavSlices::createGeometry( int slice )
                 vertices.push_back( wmath::WPosition( xPos, m_bb.second[1], m_bb.first[2]   ) );
                 for( size_t i = 0; i < nbVerts; ++i )
                 {
-                    sliceVertices->push_back( wge::wv3D2ov3( vertices[i] ) );
+                    sliceVertices->push_back( vertices[i] );
                 }
 
                 sliceGeometry->setVertexArray( sliceVertices );
@@ -641,7 +641,7 @@ osg::ref_ptr<osg::Geometry> WMNavSlices::createGeometry( int slice )
                     osg::Vec3Array* texCoords = new osg::Vec3Array;
                     for( size_t i = 0; i < nbVerts; ++i )
                     {
-                        texCoords->push_back( wge::wv3D2ov3( grid->worldCoordToTexCoord( vertices[i] ) ) );
+                        texCoords->push_back( grid->worldCoordToTexCoord( vertices[i] ) );
                     }
                     sliceGeometry->setTexCoordArray( c, texCoords );
                     ++c;
@@ -655,7 +655,7 @@ osg::ref_ptr<osg::Geometry> WMNavSlices::createGeometry( int slice )
                     osg::Vec3Array* texCoords = new osg::Vec3Array;
                     for( size_t i = 0; i < nbVerts; ++i )
                     {
-                        texCoords->push_back( wge::wv3D2ov3( grid->worldCoordToTexCoord( vertices[i] ) ) );
+                        texCoords->push_back( grid->worldCoordToTexCoord( vertices[i] ) );
                     }
                     sliceGeometry->setTexCoordArray( c, texCoords );
                     ++c;
@@ -672,7 +672,7 @@ osg::ref_ptr<osg::Geometry> WMNavSlices::createGeometry( int slice )
                 vertices.push_back( wmath::WPosition( m_bb.second[0],  yPos, m_bb.first[2]  ) );
                 for( size_t i = 0; i < nbVerts; ++i )
                 {
-                    sliceVertices->push_back( wge::wv3D2ov3( vertices[i] ) );
+                    sliceVertices->push_back( vertices[i] );
                 }
                 sliceGeometry->setVertexArray( sliceVertices );
 
@@ -684,7 +684,7 @@ osg::ref_ptr<osg::Geometry> WMNavSlices::createGeometry( int slice )
                     osg::Vec3Array* texCoords = new osg::Vec3Array;
                     for( size_t i = 0; i < nbVerts; ++i )
                     {
-                        texCoords->push_back( wge::wv3D2ov3( grid->worldCoordToTexCoord( vertices[i] ) ) );
+                        texCoords->push_back( grid->worldCoordToTexCoord( vertices[i] ) );
                     }
                     sliceGeometry->setTexCoordArray( c, texCoords );
                     ++c;
@@ -698,7 +698,7 @@ osg::ref_ptr<osg::Geometry> WMNavSlices::createGeometry( int slice )
                     osg::Vec3Array* texCoords = new osg::Vec3Array;
                     for( size_t i = 0; i < nbVerts; ++i )
                     {
-                        texCoords->push_back( wge::wv3D2ov3( grid->worldCoordToTexCoord( vertices[i] ) ) );
+                        texCoords->push_back( grid->worldCoordToTexCoord( vertices[i] ) );
                     }
                     sliceGeometry->setTexCoordArray( c, texCoords );
                     ++c;
@@ -714,7 +714,7 @@ osg::ref_ptr<osg::Geometry> WMNavSlices::createGeometry( int slice )
                 vertices.push_back( wmath::WPosition( m_bb.second[0], m_bb.first[1],  zPos ) );
                 for( size_t i = 0; i < nbVerts; ++i )
                 {
-                    sliceVertices->push_back( wge::wv3D2ov3( vertices[i] ) );
+                    sliceVertices->push_back( vertices[i] );
                 }
 
                 sliceGeometry->setVertexArray( sliceVertices );
@@ -727,7 +727,7 @@ osg::ref_ptr<osg::Geometry> WMNavSlices::createGeometry( int slice )
                     osg::Vec3Array* texCoords = new osg::Vec3Array;
                     for( size_t i = 0; i < nbVerts; ++i )
                     {
-                        texCoords->push_back( wge::wv3D2ov3( grid->worldCoordToTexCoord( vertices[i] ) ) );
+                        texCoords->push_back( grid->worldCoordToTexCoord( vertices[i] ) );
                     }
                     sliceGeometry->setTexCoordArray( c, texCoords );
                     ++c;
@@ -742,7 +742,7 @@ osg::ref_ptr<osg::Geometry> WMNavSlices::createGeometry( int slice )
 
                     for( size_t i = 0; i < nbVerts; ++i )
                     {
-                        texCoords->push_back( wge::wv3D2ov3( grid->worldCoordToTexCoord( vertices[i] ) ) );
+                        texCoords->push_back( grid->worldCoordToTexCoord( vertices[i] ) );
                     }
                     sliceGeometry->setTexCoordArray( c, texCoords );
                     ++c;
@@ -818,7 +818,7 @@ osg::ref_ptr<osg::Geometry> WMNavSlices::createCrossGeometry( int slice )
 
     for( size_t i = 0; i < vertices.size(); ++i )
     {
-        crossVertices->push_back( wge::wv3D2ov3( vertices[i] ) );
+        crossVertices->push_back( vertices[i] );
     }
 
     colorArray->push_back( osg::Vec3( 1.0f, 0.0f, 0.0f ) );