[CHANGE] As discussed yesterday math library will merge into common but stay in seperate directory

src/CMakeLists.txt

@@ -113,7 +113,6 @@ ENDIF()
 
 SET( CMAKE_CXX_FLAGS_RELWITHDEBINFO "-g -DDEBUG -O2" CACHE STRING "" FORCE )
 
-ADD_SUBDIRECTORY( math )
 ADD_SUBDIRECTORY( dataHandler )
 ADD_SUBDIRECTORY( graphicsEngine )
 ADD_SUBDIRECTORY( gui )

src/common/CMakeLists.txt

 FILE( GLOB COMMON_SRC "*.cpp" "*.h" )
 FILE( GLOB COMMON_DATASTRUCTURES_SRC "datastructures/*.cpp" "datastructures/*.h" )
 FILE( GLOB COMMON_EXCEPTIONS_SRC "exceptions/*.cpp" "exceptions/*.h" )
+FILE( GLOB MATH_SRC "math/*.cpp" "math/*.h" )
+FILE( GLOB FIBERSIMILARITY_SRC "math/fiberSimilarity/*.cpp" "math/fiberSimilarity/*.h" )
 
 ADD_SUBDIRECTORY( datastructures )
 ADD_SUBDIRECTORY( constraints )
+ADD_SUBDIRECTORY( math )
 
-ADD_LIBRARY( common ${COMMON_SRC} ${COMMON_DATASTRUCTURES_SRC} ${COMMON_EXCEPTIONS_SRC} )
-TARGET_LINK_LIBRARIES( common ${Boost_LIBRARIES} math )
+ADD_LIBRARY( common ${COMMON_SRC} ${COMMON_DATASTRUCTURES_SRC} ${COMMON_EXCEPTIONS_SRC} ${MATH_SRC} ${FIBERSIMILARITY_SRC} )
+TARGET_LINK_LIBRARIES( common ${Boost_LIBRARIES} )
 
 # Unit tests
 IF( OW_COMPILE_TESTS )

src/common/WPropertyTypes.h

@@ -33,7 +33,7 @@
 
 #include <boost/filesystem.hpp>
 
-#include "../math/WPosition.h"
+#include "math/WPosition.h"
 #include "WColor.h"
 
 template < typename T >

src/common/datastructures/WTriangleMesh.h

@@ -27,8 +27,8 @@
 
 #include <vector>
 
-#include "../../math/WPosition.h"
-#include "../../math/WVector3D.h"
+#include "../math/WPosition.h"
+#include "../math/WVector3D.h"
 
 
 /**

src/common/datastructures/test/WTriangleMesh_test.h

@@ -30,7 +30,7 @@
 #include <cxxtest/TestSuite.h>
 
 #include "../WTriangleMesh.h"
-#include "../../../math/WVector3D.h"
+#include "../../math/WVector3D.h"
 
 
 /**

src/math/CMakeLists.txt → src/common/math/CMakeLists.txt

@@ -3,12 +3,10 @@ ADD_SUBDIRECTORY( fiberSimilarity )
 FILE( GLOB MATH_SRC "*.cpp" "*.h" )
 FILE( GLOB FIBERSIMILARITY_SRC "fiberSimilarity/*.cpp" "fiberSimilarity/*.h" )
 
-ADD_LIBRARY( math ${MATH_SRC} ${FIBERSIMILARITY_SRC} )
-
 # Unit tests
 IF( OW_COMPILE_TESTS )
   CXXTEST_ADD_TESTS_FROM_LIST( "${MATH_SRC}"
-                               "math;common"
+                               "common"
                                "WMath.cpp" # this declares only a namespace
                              )
 ENDIF( OW_COMPILE_TESTS )

src/math/WLine.cpp → src/common/math/WLine.cpp

@@ -26,9 +26,9 @@
 #include <iostream>
 #include <vector>
 
-#include "../common/WLimits.h"
-#include "../common/WStringUtils.h"
-#include "../common/exceptions/WOutOfBounds.h"
+#include "../WLimits.h"
+#include "../WStringUtils.h"
+#include "../exceptions/WOutOfBounds.h"
 #include "WLine.h"
 #include "WPosition.h"
 

src/math/WLine.h → src/common/math/WLine.h

@@ -29,7 +29,7 @@
 #include <iostream>
 #include <vector>
 
-#include "../common/WMixinVector.h"
+#include "../WMixinVector.h"
 #include "WPosition.h"
 
 // we need this to find the WLineTest class which is not inside wmath namespace

src/math/WValue.h → src/common/math/WValue.h

@@ -29,7 +29,7 @@
 #include <cmath>
 #include <vector>
 
-#include "../common/WStringUtils.h"
+#include "../WStringUtils.h"
 
 namespace wmath
 {

src/math/fiberSimilarity/CMakeLists.txt → src/common/math/fiberSimilarity/CMakeLists.txt

@@ -3,7 +3,7 @@ FILE( GLOB FIBERSIMILARITY_SRC "*.cpp" "*.h" )
 # Unit tests
 IF( OW_COMPILE_TESTS )
   CXXTEST_ADD_TESTS_FROM_LIST( "${FIBERSIMILARITY_SRC}"
-                               "math;common"
+                               "common"
                                "WFiberSimilarity.cpp" # This is just an interface
                               )
 ENDIF( OW_COMPILE_TESTS )

src/math/fiberSimilarity/WZhangMetric.cpp → src/common/math/fiberSimilarity/WZhangMetric.cpp

@@ -27,7 +27,7 @@
 #include <vector>
 
 #include "WZhangMetric.h"
-#include "../../common/WLimits.h"
+#include "../../WLimits.h"
 
 WZhangMetric::WZhangMetric( double thresholdSquare )
     : m_thresholdSquare( thresholdSquare )

src/math/test/WFiberTraits.h → src/common/math/test/WFiberTraits.h

@@ -30,7 +30,7 @@
 #include <cxxtest/TestSuite.h>
 #include <cxxtest/ValueTraits.h>
 
-#include "../../common/test/WTraitsBase.h"
+#include "../../test/WTraitsBase.h"
 #include "../WFiber.h"
 
 #ifdef CXXTEST_RUNNING

src/math/test/WLineTraits.h → src/common/math/test/WLineTraits.h

@@ -30,7 +30,7 @@
 #include <cxxtest/TestSuite.h>
 #include <cxxtest/ValueTraits.h>
 
-#include "../../common/test/WTraitsBase.h"
+#include "../../test/WTraitsBase.h"
 #include "../WLine.h"
 
 #ifdef CXXTEST_RUNNING

src/math/test/WLine_test.h → src/common/math/test/WLine_test.h

@@ -30,8 +30,8 @@
 
 #include <cxxtest/TestSuite.h>
 
-#include "../../common/WLimits.h"
-#include "../../common/exceptions/WOutOfBounds.h"
+#include "../../WLimits.h"
+#include "../../exceptions/WOutOfBounds.h"
 #include "../WLine.h"
 #include "WLineTraits.h"
 #include "WPositionTraits.h"

src/math/test/WPositionTraits.h → src/common/math/test/WPositionTraits.h

@@ -30,7 +30,7 @@
 #include <cxxtest/TestSuite.h>
 #include <cxxtest/ValueTraits.h>
 
-#include "../../common/test/WTraitsBase.h"
+#include "../../test/WTraitsBase.h"
 #include "../WPosition.h"
 
 #ifdef CXXTEST_RUNNING

src/math/test/WVector3DTraits.h → src/common/math/test/WVector3DTraits.h

@@ -30,7 +30,7 @@
 #include <cxxtest/TestSuite.h>
 #include <cxxtest/ValueTraits.h>
 
-#include "../../common/test/WTraitsBase.h"
+#include "../../test/WTraitsBase.h"
 #include "../WVector3D.h"
 
 #ifdef CXXTEST_RUNNING

src/dataHandler/CMakeLists.txt

@@ -13,10 +13,10 @@ IF( CMAKE_GENERATOR MATCHES "Visual Studio" )
     FILE( GLOB EXCLUDE_biosig "io/*Biosig.cpp" "io/*Biosig.h" )
     LIST( REMOVE_ITEM DATAHANDLER_IO_SRC ${EXCLUDE_biosig} )
     ADD_LIBRARY( dataHandler ${DATAHANDLER_SRC} ${DATAHANDLER_EXCEPTIONS_SRC} ${DATAHANDLER_IO_SRC} ${DATAHANDLER_DATASTRUCTURES_SRC} )
-    TARGET_LINK_LIBRARIES( dataHandler common math ${Boost_LIBRARIES} niftiio libeep ${OPENSCENEGRAPH_LIBRARIES})
+    TARGET_LINK_LIBRARIES( dataHandler common ${Boost_LIBRARIES} niftiio libeep ${OPENSCENEGRAPH_LIBRARIES})
 ELSE()
     ADD_LIBRARY( dataHandler ${DATAHANDLER_SRC} ${DATAHANDLER_EXCEPTIONS_SRC} ${DATAHANDLER_IO_SRC} ${DATAHANDLER_DATASTRUCTURES_SRC} )
-    TARGET_LINK_LIBRARIES( dataHandler common math ${Boost_LIBRARIES} niftiio biosig libeep ${OPENSCENEGRAPH_LIBRARIES})
+    TARGET_LINK_LIBRARIES( dataHandler common ${Boost_LIBRARIES} niftiio biosig libeep ${OPENSCENEGRAPH_LIBRARIES})
 ENDIF()
 # Unit tests
 IF( OW_COMPILE_TESTS )

src/dataHandler/WDataSetFiberVector.cpp

@@ -27,7 +27,7 @@
 #include <vector>
 
 #include "../common/WLogger.h"
-#include "../math/WFiber.h"
+#include "../common/math/WFiber.h"
 #include "WDataSet.h"
 #include "WDataSetFiberVector.h"
 

src/dataHandler/WDataSetFiberVector.h

@@ -30,7 +30,7 @@
 
 #include <boost/shared_ptr.hpp>
 
-#include "../math/WFiber.h"
+#include "../common/math/WFiber.h"
 #include "WDataSet.h"
 #include "WDataSetFibers.h"
 

src/dataHandler/WDataSetFibers.h

@@ -30,7 +30,7 @@
 
 #include <boost/shared_ptr.hpp>
 
-#include "../math/WPosition.h"
+#include "../common/math/WPosition.h"
 
 #include "WDataSet.h"
 

src/dataHandler/WEEG.h

@@ -30,7 +30,7 @@
 #include <vector>
 #include "WRecording.h"
 #include "../common/WPrototyped.h"
-#include "../math/WPosition.h"
+#include "../common/math/WPosition.h"
 
 
 ///======================================

src/dataHandler/WGrid.h

@@ -28,7 +28,7 @@
 #include <cstddef>
 #include <utility>
 
-#include "../math/WPosition.h"
+#include "../common/math/WPosition.h"
 
 /**
  * Base class to all grid types, e.g. a regular grid.

src/dataHandler/WGridRegular3D.cpp

@@ -26,7 +26,7 @@
 #include <vector>
 
 #include "../common/exceptions/WOutOfBounds.h"
-#include "../math/WLinearAlgebraFunctions.h"
+#include "../common/math/WLinearAlgebraFunctions.h"
 #include "WGridRegular3D.h"
 
 using wmath::WVector3D;

src/dataHandler/WGridRegular3D.h

@@ -32,9 +32,9 @@
 
 #include <osg/Vec3>
 
-#include "../math/WMatrix.h"
-#include "../math/WPosition.h"
-#include "../math/WVector3D.h"
+#include "../common/math/WMatrix.h"
+#include "../common/math/WPosition.h"
+#include "../common/math/WVector3D.h"
 #include "WGrid.h"
 
 /**

src/dataHandler/WValueSet.h

@@ -31,7 +31,7 @@
 
 #include "WValueSetBase.h"
 #include "WDataHandlerEnums.h"
-#include "../math/WValue.h"
+#include "../common/math/WValue.h"
 
 /**
  * Base Class for all value set types.

src/dataHandler/io/WLoaderNIfTI.h

@@ -30,7 +30,7 @@
 #include <boost/shared_ptr.hpp>
 
 #include "../WLoader.h"
-#include "../../math/WMatrix.h"
+#include "../../common/math/WMatrix.h"
 
 #include "nifti/nifti1_io.h"
 

src/dataHandler/io/test/WLoaderFibers_test.h

@@ -35,7 +35,7 @@
 #include <cxxtest/TestSuite.h>
 
 #include "../../../common/test/WStreamPosTraits.h"
-#include "../../../math/test/WFiberTraits.h"
+#include "../../../common/math/test/WFiberTraits.h"
 #include "../WLoaderFibers.h"
 
 /**

src/dataHandler/test/WDataSetFiberVector_test.h

@@ -31,7 +31,7 @@
 #include <cxxtest/TestSuite.h>
 
 #include "../WDataSetFiberVector.h"
-#include "../../math/WPosition.h"
+#include "../../common/math/WPosition.h"
 
 /**
  * Unit tests our fiber dataset class

src/dataHandler/test/WGridRegular3D_test.h

@@ -35,7 +35,7 @@
 #include <cxxtest/TestSuite.h>
 
 #include "../../common/exceptions/WOutOfBounds.h"
-#include "../../math/test/WVector3DTraits.h"
+#include "../../common/math/test/WVector3DTraits.h"
 #include "../WGridRegular3D.h"
 
 using wmath::WVector3D;

src/graphicsEngine/CMakeLists.txt

@@ -9,7 +9,7 @@ TARGET_LINK_LIBRARIES( ge common ${OPENGL_gl_LIBRARY} ${OPENGL_glu_LIBRARY} ${OP
 
 # Unit tests
 IF( OW_COMPILE_TESTS )
-  CXXTEST_ADD_TESTS_FROM_LIST( "${GE_SRC}" "ge;math"
+  CXXTEST_ADD_TESTS_FROM_LIST( "${GE_SRC}" "ge"
           "WGESignals.cpp"
           "WGraphicsEngine.cpp"
           "WGEScene.cpp"

src/graphicsEngine/WGEGeodeUtils.cpp

@@ -32,7 +32,7 @@
 
 #include "WGEGeodeUtils.h"
 #include "WGEUtils.h"
-#include "../math/WPosition.h"
+#include "../common/math/WPosition.h"
 
 
 osg::ref_ptr< osg::Geode > wge::generateBoundingBoxGeode( const wmath::WPosition& pos1, const wmath::WPosition& pos2, const WColor& color )

src/graphicsEngine/WGEGeodeUtils.h

@@ -29,8 +29,8 @@
 
 #include "../common/datastructures/WTriangleMesh.h"
 #include "../common/WColor.h"
-#include "../math/WPosition.h"
-#include "../math/WLine.h"
+#include "../common/math/WPosition.h"
+#include "../common/math/WLine.h"
 
 
 namespace wge

src/graphicsEngine/WGEGeometryUtils.cpp

@@ -31,7 +31,7 @@
 #include "exceptions/WGEException.h"
 #include "WGEGeometryUtils.h"
 #include "WGEUtils.h"
-#include "../math/WPosition.h"
+#include "../common/math/WPosition.h"
 
 
 osg::ref_ptr< osg::Vec3Array > wge::generateCuboidQuads( const std::vector< wmath::WPosition >& corners )

src/graphicsEngine/WGEGeometryUtils.h

@@ -30,7 +30,7 @@
 #include <osg/Array>
 
 #include "../common/datastructures/WTriangleMesh.h"
-#include "../math/WPosition.h"
+#include "../common/math/WPosition.h"
 
 
 namespace wge

src/graphicsEngine/WGEUtils.cpp

@@ -28,7 +28,7 @@
 
 #include <GL/glu.h>
 
-#include "../math/WPosition.h"
+#include "../common/math/WPosition.h"
 #include "WGEUtils.h"
 
 osg::ref_ptr< osg::Vec3Array > wge::osgVec3Array( const std::vector< wmath::WPosition >& posArray )

src/graphicsEngine/WGEUtils.h

@@ -33,7 +33,7 @@
 #include <osg/Camera>
 
 #include "../common/WColor.h"
-#include "../math/WPosition.h"
+#include "../common/math/WPosition.h"
 
 namespace wge
 {

src/graphicsEngine/WGraphicsEngine.cpp

@@ -40,7 +40,7 @@
 #include "../common/WColor.h"
 #include "../common/WLogger.h"
 #include "../common/WPreferences.h"
-#include "../math/WPosition.h"
+#include "../common/math/WPosition.h"
 #include "WGEViewer.h"
 #include "WGraphicsEngine.h"
 #include "exceptions/WGEInitFailed.h"

src/graphicsEngine/WGraphicsEngine.h

@@ -46,7 +46,7 @@
 
 #include "../common/WThreadedRunner.h"
 #include "../common/WColor.h"
-#include "../math/WPosition.h"
+#include "../common/math/WPosition.h"
 #include "WGEGraphicsWindow.h"
 #include "WGEScene.h"
 #include "WGEViewer.h"

src/graphicsEngine/WPickHandler.h

@@ -46,7 +46,7 @@
 #include <osg/ShapeDrawable>
 #include <osgText/Text>
 
-#include "../math/WPosition.h"
+#include "../common/math/WPosition.h"
 #include "WPickInfo.h"
 
 /**

src/graphicsEngine/WPickInfo.h

@@ -28,8 +28,8 @@
 #include <string>
 #include <utility>
 
-#include "../math/WPosition.h"
-#include "../math/WVector3D.h"
+#include "../common/math/WPosition.h"
+#include "../common/math/WVector3D.h"
 
 /**
  * Encapsulates info for pick action.

src/graphicsEngine/WROIBox.h

@@ -30,7 +30,7 @@
 
 #include <boost/thread.hpp>
 
-#include "../math/WPosition.h"
+#include "../common/math/WPosition.h"
 #include "WPickHandler.h"
 #include "WGEViewer.h"
 

src/kernel/CMakeLists.txt

@@ -6,7 +6,7 @@ ADD_SUBDIRECTORY( exceptions )
 FILE( GLOB KERNEL_EXCEPTIONS_SRC "exceptions/*.cpp" "exceptions/*.h" )
 
 ADD_LIBRARY( kernel ${KERNEL_SRC} ${MODULES_SRC} ${KERNEL_EXCEPTIONS_SRC} )
-TARGET_LINK_LIBRARIES( kernel common dataHandler ge math ${OPENSCENEGRAPH_LIBRARIES} )
+TARGET_LINK_LIBRARIES( kernel common dataHandler ge ${OPENSCENEGRAPH_LIBRARIES} )
 
 
 # Unit tests

src/modules/applyMask/WMApplyMask.h

@@ -36,7 +36,7 @@
 #include "../../kernel/WModule.h"
 #include "../../kernel/WModuleInputData.h"
 
-#include "../../math/WVector3D.h"
+#include "../../common/math/WVector3D.h"
 
 class WPickHandler;
 

src/modules/boundingBox/WMBoundingBox.cpp

@@ -34,8 +34,8 @@
 #include "../../dataHandler/WGridRegular3D.h"
 #include "../../graphicsEngine/WGEGeodeUtils.h"
 #include "../../kernel/WKernel.h"
-#include "../../math/WPosition.h"
-#include "../../math/WVector3D.h"
+#include "../../common/math/WPosition.h"
+#include "../../common/math/WVector3D.h"
 #include "../data/WMData.h"
 #include "WMBoundingBox.h"
 #include "boundingbox.xpm"

src/modules/boundingBox/WMBoundingBox.h

@@ -36,7 +36,7 @@
 #include "../../kernel/WModule.h"
 #include "../../kernel/WModuleInputData.h"
 
-#include "../../math/WVector3D.h"
+#include "../../common/math/WVector3D.h"
 
 class WPickHandler;
 

src/modules/connectomeView/WMConnectomeView.cpp

@@ -41,7 +41,7 @@
 
 #include "../../common/WProgress.h"
 #include "../../common/WPreferences.h"
-#include "../../math/WVector3D.h"
+#include "../../common/math/WVector3D.h"
 #include "../../dataHandler/WSubject.h"
 #include "../../dataHandler/WGridRegular3D.h"
 #include "../../dataHandler/WDataTexture3D.h"

src/modules/coordinateSystem/WCoordConverter.h

@@ -25,8 +25,8 @@
 #ifndef WCOORDCONVERTER_H
 #define WCOORDCONVERTER_H
 
-#include "../../math/WVector3D.h"
-#include "../../math/WMatrix.h"
+#include "../../common/math/WVector3D.h"
+#include "../../common/math/WMatrix.h"
 
 using wmath::WMatrix;
 using wmath::WVector3D;

src/modules/coordinateSystem/WTalairachConverter.cpp

@@ -25,7 +25,7 @@
 #include <cassert>
 
 #include "WTalairachConverter.h"
-#include "../../math/WLinearAlgebraFunctions.h"
+#include "../../common/math/WLinearAlgebraFunctions.h"
 
 WTalairachConverter::WTalairachConverter( wmath::WVector3D ac, wmath::WVector3D pc, wmath::WVector3D ihp ) :
     m_rotMat( 3, 3 ),

src/modules/coordinateSystem/WTalairachConverter.h

@@ -25,8 +25,8 @@
 #ifndef WTALAIRACHCONVERTER_H
 #define WTALAIRACHCONVERTER_H
 
-#include "../../math/WVector3D.h"
-#include "../../math/WMatrix.h"
+#include "../../common/math/WVector3D.h"
+#include "../../common/math/WMatrix.h"
 
 /**
  * class to provide conversions between world or voxel space coordinates und talairach coordinates

src/modules/dataTypeConversion/WMDataTypeConversion.cpp

@@ -35,8 +35,8 @@
 #include "../../common/WProgress.h"
 #include "../../dataHandler/WGridRegular3D.h"
 #include "../../kernel/WKernel.h"
-#include "../../math/WPosition.h"
-#include "../../math/WVector3D.h"
+#include "../../common/math/WPosition.h"
+#include "../../common/math/WVector3D.h"
 #include "../data/WMData.h"
 #include "WMDataTypeConversion.h"
 #include "datatypeconversion.xpm"

src/modules/dataTypeConversion/WMDataTypeConversion.h

@@ -36,7 +36,7 @@
 #include "../../kernel/WModule.h"
 #include "../../kernel/WModuleInputData.h"
 
-#include "../../math/WVector3D.h"
+#include "../../common/math/WVector3D.h"
 
 /**
  * Provides a new field with the approximately the same data, but with another data type. E.g., it

src/modules/fiberClustering/WMFiberClustering.cpp

@@ -46,8 +46,8 @@
 #include "../../dataHandler/io/WWriterLookUpTableVTK.h"
 #include "../../graphicsEngine/WGEUtils.h"
 #include "../../kernel/WKernel.h"
-#include "../../math/WFiber.h"
-#include "../../math/fiberSimilarity/WDLTMetric.h"
+#include "../../common/math/WFiber.h"
+#include "../../common/math/fiberSimilarity/WDLTMetric.h"
 #include "WMFiberClustering.h"
 
 WMFiberClustering::WMFiberClustering()

src/modules/fiberClustering/WMFiberClustering.h

@@ -38,7 +38,7 @@
 #include "../../graphicsEngine/WGEGroupNode.h"
 #include "../../kernel/WModule.h"
 #include "../../kernel/WModuleInputData.h"
-#include "../../math/WFiber.h"
+#include "../../common/math/WFiber.h"
 
 /**
  * Test module for Clustering fibers

src/modules/fiberCulling/WMFiberCulling.cpp

@@ -36,8 +36,8 @@
 #include "../../dataHandler/WSubject.h"
 #include "../../dataHandler/io/WWriterFiberVTK.h"
 #include "../../kernel/WKernel.h"
-#include "../../math/WFiber.h"
-#include "../../math/fiberSimilarity/WDSTMetric.h"
+#include "../../common/math/WFiber.h"
+#include "../../common/math/fiberSimilarity/WDSTMetric.h"
 #include "WMFiberCulling.h"
 
 WMFiberCulling::WMFiberCulling()

src/modules/fiberCulling/WMFiberCulling.h

@@ -33,7 +33,7 @@
 #include "../../dataHandler/WDataSetFiberVector.h"
 #include "../../kernel/WModule.h"
 #include "../../kernel/WModuleInputData.h"
-#include "../../math/WFiber.h"
+#include "../../common/math/WFiber.h"
 
 /**