[MERGE] rev4170

9f970e5a · Robert Frohl · 5ac1f205 · c465e29c · 9f970e5a · 9f970e5a
Commit 9f970e5a authored Feb 21, 2011 by Robert Frohl
20 changed files
--- a/.hg_notify.hgml
+++ b/.hg_notify.hgml
 [usersubs]
-wiebel@informatik.uni-leipzig.de = *
-math@informatik.uni-leipzig.de = *
-ebaum@informatik.uni-leipzig.de = *
-reichenbach@informatik.uni-leipzig.de = *
-philips@zimbra.cbs.mpg.de = *
\ No newline at end of file
+all-openwalnut-commits@lists.informatik.uni-leipzig.de = *
\ No newline at end of file
--- a/.hgchurn
+++ b/.hgchurn
 wiebel Alexander_Wiebel
 wiebel@hegel.informatik.uni-leipzig.de Alexander_Wiebel
 openwalnut@dergrosse.de Alexander_Wiebel
+wiebel@openwalnut.org Alexander_Wiebel
 wiebel_openwalnut@dergrosse.de Alexander_Wiebel
 wiebel@bsv_2008a Alexander_Wiebel
 math Mathias_Goldau
 lmath@voltaire.informatik.uni-leipzig.de Mathias_Goldau
 math@informatik.uni-leipzig.de Mathias_Goldau
+schurade@spinat.cbs.mpg.de Ralph_Schurade
 schurade Ralph_Schurade
 ebaum Sebastian_Eichelbaum
 eichelbaum@informatik.uni-leipzig.de Sebastian_Eichelbaum
@@ -15,4 +17,12 @@ hlawitschka@ucdavis.edu Mario_Hlawitschka
 mai02igw@informatik.uni-leipzig.de Robin_Ledig
 mai02ifw@informatik.uni-leipzig.de Robin_Ledig
 mai02igw@studserv.uni-leipzig.de Robin_Ledig
-heine@informatik.uni-leipzig.de Christian_Heine
\ No newline at end of file
+heine@informatik.uni-leipzig.de Christian_Heine
+reichenbach@berkeley.informatik.uni-leipzig.de Andre_Reichenbach
+reichenbach Andre_Reichenbach
+philips@informatik.uni-leipzig.de Stefan_Philips
+frohl.robert@googlemail.com Robert_Frohl
+dirk_albrecht@gmx.net Dirk_Albrecht
+albrecht Dirk_Albrecht
+mstuber Marcus_Stuber
+skiunke Sebastian_Kiunke
\ No newline at end of file
--- a/build/.README
+++ b/build/.README
 This directory is intended to serve as the place where one can compile OpenWalnut.

-This .README file is in the build directory so that the directory will be recognized and created by mercurial. Only remove it if you know what you are doing or if the behavior of mercurial concerning empty directories has changed.
\ No newline at end of file
+This .README file is in the build directory so that the directory will be recognized and created by mercurial (hg). Only remove it if you know what you are doing or if the behavior of mercurial concerning empty directories has changed.
\ No newline at end of file
--- a/doc/INSTALL
+++ b/doc/INSTALL
@@ -7,10 +7,7 @@ the currect working directory to be project's main directory,
 the following steps should do the trick:

 > cd build
-> ccmake ../src
-PRESS 'c' for configuration
-PRESS 'c' again for further configuration
-PRESS 'g' to generate the build system including the Makefiles.
+> cmake ../src
 > make

 Now the subdirectory "bin" of the "build" directory should contain an executable named walnut.

--- a/doc/developer/doxygenConfig
+++ b/doc/developer/doxygenConfig
@@ -31,7 +31,7 @@ PROJECT_NAME           = OpenWalnut
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.

-PROJECT_NUMBER         = 1.0+
+PROJECT_NUMBER         = 1.1+

 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
 # base path where the generated documentation will be put.
@@ -1030,7 +1030,7 @@ FORMULA_FONTSIZE       = 10
 # typically be disabled. For large projects the javascript based search engine
 # can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution.

-SEARCHENGINE           = NO
+SEARCHENGINE           = YES

 # When the SERVER_BASED_SEARCH tag is enabled the search engine will be implemented using a PHP enabled web server instead of at the web client using Javascript. Doxygen will generate the search PHP script and index
 # file to put on the web server. The advantage of the server based approach is that it scales better to large projects and allows full text search. The disadvances is that it is more difficult to setup
@@ -1324,7 +1324,11 @@ INCLUDE_FILE_PATTERNS  =

 PREDEFINED             = OUTLINE \
                         _GNU_SOURCE \
-                         NODEBUG
+                         NODEBUG \
+                         WGE_EXPORT \
+                         OWCOMMON_EXPORT \
+                         OWDATAHANDLER_EXPORT \
+                         OWKERNEL_EXPORT 

 # If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then
 # this tag can be used to specify a list of macro names that should be expanded.

--- a/doc/developer/doxygenConfigFull
+++ b/doc/developer/doxygenConfigFull
@@ -31,7 +31,7 @@ PROJECT_NAME           = OpenWalnut
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.

-PROJECT_NUMBER         = 1.0+
+PROJECT_NUMBER         = 1.1+

 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
 # base path where the generated documentation will be put.
@@ -1030,7 +1030,7 @@ FORMULA_FONTSIZE       = 10
 # typically be disabled. For large projects the javascript based search engine
 # can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution.

-SEARCHENGINE           = NO
+SEARCHENGINE           = YES

 # When the SERVER_BASED_SEARCH tag is enabled the search engine will be implemented using a PHP enabled web server instead of at the web client using Javascript. Doxygen will generate the search PHP script and index
 # file to put on the web server. The advantage of the server based approach is that it scales better to large projects and allows full text search. The disadvances is that it is more difficult to setup
@@ -1324,7 +1324,11 @@ INCLUDE_FILE_PATTERNS  =

 PREDEFINED             = OUTLINE \
                         _GNU_SOURCE \
-                         NODEBUG
+                         NODEBUG \
+                         WGE_EXPORT \
+                         OWCOMMON_EXPORT \
+                         OWDATAHANDLER_EXPORT \
+                         OWKERNEL_EXPORT 

 # If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then
 # this tag can be used to specify a list of macro names that should be expanded.

--- a/doc/user/walnut.cfg.devel
+++ b/doc/user/walnut.cfg.devel
@@ -43,17 +43,25 @@ compatiblesToolBarStyle = 0 # this pref allows the compatibles toolbar to have a
 # 2 -> left
 # 3 -> right
 # 4 -> hide completely
-# 5 -> inside the dataset browser ( not possible for compatiblesToolBarPos! This will be mapped to right (=3) )
+# 5 -> inside the control panel ( not possible for compatiblesToolBarPos! This will be mapped to right (=3) )
 toolBarPos = 0 # default position of the toolbars
 compatiblesToolBarPos = 0 # position of the compatibles toolbar (overrides toolBarPos)

 ####################################################################
-# Dataset Browser
+# Control panel

 # combineTreeAndRoiAndTextureSorter = yes # should the module tree, ROI tree and the Texture Sorter be combined in ONE Tab widget?
-# dsbWidth = 400  # the width of the dataset browser
-# dsbInvisibleByDefault = yes # hide the dataset browser on startup. Can be shown using F9.
-# dsbFloatingByDefault = yes  # should the dataset browser be undocked on startup?
+# dsbWidth = 400  # the width of the control panel
+# dsbInvisibleByDefault = yes # hide the control panel on startup. Can be shown using F9.
+# dsbFloatingByDefault = yes  # should the control panel be undocked on startup?
+
+# Here you can put any key sequence you would like to result in removing modules or ROIs
+# Examples: 
+# deleteKey = Backspace
+# deleteKey = Ctrl+J
+# deleteKey = B
+deleteModuleKey = Backspace
+deleteROIKey = Del

 ####################################################################
 # Other GUI settings
@@ -65,4 +73,4 @@ compatiblesToolBarPos = 0 # position of the compatibles toolbar (overrides toolB
 # bgColor.g = .9 # background color (green part)
 # bgColor.b = .9 # background color (blue part)
 zoomTrackballManipulator.allowThrow = yes # allow the auto-rotation thing when "throwing" an object with the mouse
-# multiThreadedViewers = no # Use multiple threads for the multiple viewers. Causes hanging on some machines when opening a new view.
+multiThreadedViewers = no # Use multiple threads for the multiple viewers. Causes hanging on some machines when opening a new view.
--- a/doc/user/walnut.cfg.mpi
+++ b/doc/user/walnut.cfg.mpi
 ## This is a sample configuration file for OpenWalnut.
 ## Uncomment the options you are interested in.

-[general]
-allowOnlyOneFiberDataSet = yes # This will prevent you from accidently loading multiple fiber data sets.
-
 [modules]
 ## use this to specify the default module to add during load.
 ## It is a comma seperated list. If this is not specified the 
@@ -12,7 +9,7 @@ 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,Fiber Display,Read Spherical Harmonics,Navigation Slices,Deterministic Tract Clustering using Gaussian Processes,Deterministic Tract to Gaussian Process Converter,Cluster Param Display,Write Tracts,Fiber Resampling,Teem Glyphs

 ## 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
@@ -49,17 +46,25 @@ compatiblesToolBarStyle = 0 # this pref allows the compatibles toolbar to have a
 # 2 -> left
 # 3 -> right
 # 4 -> hide completely
-# 5 -> inside the dataset browser ( not possible for compatiblesToolBarPos! This will be mapped to right (=3) )
+# 5 -> inside the control panel ( not possible for compatiblesToolBarPos! This will be mapped to right (=3) )
 toolBarPos = 0 # default position of the toolbars
 compatiblesToolBarPos = 0 # position of the compatibles toolbar (overrides toolBarPos)

 ####################################################################
-# Dataset Browser
+# Control panel

 # combineTreeAndRoiAndTextureSorter = yes # should the module tree, ROI tree and the Texture Sorter be combined in ONE Tab widget?
-# dsbWidth = 400  # the width of the dataset browser
-# dsbInvisibleByDefault = yes # hide the dataset browser on startup. Can be shown using F9.
-# dsbFloatingByDefault = yes  # should the dataset browser be undocked on startup?
+# dsbWidth = 400  # the width of the control panel
+# dsbInvisibleByDefault = yes # hide the control panel on startup. Can be shown using F9.
+# dsbFloatingByDefault = yes  # should the control panel be undocked on startup?
+
+# Here you can put any key sequence you would like to result in removing modules or ROIs
+# Examples: 
+# deleteKey = Backspace
+# deleteKey = Ctrl+J
+# deleteKey = B
+deleteModuleKey = Backspace
+deleteROIKey = Del

 ####################################################################
 # Other GUI settings
@@ -70,5 +75,5 @@ compatiblesToolBarPos = 0 # position of the compatibles toolbar (overrides toolB
 # bgColor.r = .9 # background color (red part)
 # bgColor.g = .9 # background color (green part)
 # bgColor.b = .9 # background color (blue part)
-# zoomTrackballManipulator.allowThrow = yes # allow the auto-rotation thing when "throwing" an object with the mouse
+zoomTrackballManipulator.allowThrow = no # allow the auto-rotation thing when "throwing" an object with the mouse
 multiThreadedViewers = no # Use multiple threads for the multiple viewers. Causes hanging on some machines when opening a new view.
--- a/scripts/bin/walnut-pyclewn
+++ b/scripts/bin/walnut-pyclewn
+#!/bin/sh
+
+# This script allows you to use PyClewn (Vim GDB integration) with walnut.
+
+# get path of this script
+BINDIR=`dirname "$0"`
+SRCDIR=$BINDIR  # we assume this. We test lateron whether this
+
+# we assume that your source dir is two or tree levels up. Setting the working directory to the source dir
+# eases file browsing vim later
+if [ -d "$BINDIR/../../src" ]; then
+    SRCDIR="$BINDIR/../../src"
+else
+    if [ -d "$BINDIR/../../../src" ]; then
+        SRCDIR="$BINDIR/../../../src"
+    else
+        echo "Could not find source dir." # this is not really critical.
+    fi
+fi
+
+# run walnut
+pyclewn -c "-c \"cd $SRCDIR\"" -a $BINDIR/walnut "$*"
+
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
 CMAKE_MINIMUM_REQUIRED(VERSION 2.6)
 PROJECT( OpenWalnut )

+# guard against in-source builds
+IF( ${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR} )
+  MESSAGE( FATAL_ERROR "In-source builds not allowed. Please make a new directory (called a build directory) and run CMake from there. (you may need to remove CMakeCache.txt" )
+ENDIF()
+
+
+
 # append search path for FindModules:
 #------------------------------------
 LIST( APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/../tools/CMakeModules )
 # include custom CMake commands like assert
 INCLUDE( ${PROJECT_SOURCE_DIR}/../tools/CMakeModules/Utils.cmake )
+INCLUDE( ${PROJECT_SOURCE_DIR}/../tools/CMakeModules/OnlyOneBuildFile.cmake )

 # mimic layout of install dir for build:
 #----------------------------------------
@@ -27,6 +35,17 @@ IF( CMAKE_GENERATOR MATCHES "Visual Studio" )
  INCLUDE_DIRECTORIES( "${PROJECT_SOURCE_DIR}/common/platformDependent/visualStudio/" )
 ENDIF()

+OPTION( OW_BUILD_AS_ONE_BIG_FILE "Build every library as one big cpp" OFF )
+INCLUDE( FindPythonInterp )
+
+# define libnames 
+SET( OWCommonName "OWcommon" )
+SET( OWDatahandlerName "OWdataHandler" )
+SET( OWgeName "OWge" )
+SET( OWguiName "OWgui" )
+SET( OWguiqt4Name "OWguiqt4" )
+SET( OWKernelName "OWkernel" )
+SET( OWmodulesPrefix "OWmodule" )

 # Package dependencies:
 #----------------------
@@ -87,7 +106,7 @@ ELSE()
  IF( NOT VERSION LESS 2.6.3 )
    SET ( CMAKE_PREFIX_PATH "$ENV{ProgramFiles}/OpenSceneGraph" )
  ENDIF()
-  FIND_PACKAGE( OpenSceneGraph ${MIN_OSG_VERSION} REQUIRED osgUtil osgDB osgViewer osgText osgGA osgSim )
+  FIND_PACKAGE( OpenSceneGraph ${MIN_OSG_VERSION} REQUIRED osgUtil osgDB osgViewer osgText osgGA osgSim osgWidget )
  INCLUDE_DIRECTORIES( ${OPENSCENEGRAPH_INCLUDE_DIRS} )
 ENDIF()

@@ -103,16 +122,78 @@ ENDIF()
 FIND_PACKAGE( OSSIM QUIET )
 IF( OSSIM_FOUND )
  MESSAGE( STATUS "Found OSSIM." )
-  ADD_DEFINITIONS( -DUSEOSSIM )
+  OPTION( OW_USE_OSSIM "Use the ossim library for singular value decomposition." OFF )
  INCLUDE_DIRECTORIES( ${OSSIM_INCLUDE_DIR} )
-  LINK_LIBRARIES( ${OSSIM_LIBRARY} )
-# TODO(math): is an entry in link directories necessary?
-#   LINK_DIRECTORIES( ${OSSIM_LIBDIR} )
+  LINK_LIBRARIES( ${OSSIM_LIBRARY} ) # this is necessary since you may install OSSIM not in the default library path
  MARK_AS_ADVANCED( OSSIM_INCLUDEDIR )
  MARK_AS_ADVANCED( OSSIM_LIBRARIES )
-#   MARK_AS_ADVANCED( OSSIM_LIBDIR )
+  IF( OW_USE_OSSIM )
+    ADD_DEFINITIONS( -DOW_USE_OSSIM )
+  ENDIF()
 ENDIF()

+# insight toolkit (for image segmentation and registration)
+#----------------------------------------------------------
+FIND_PACKAGE( ITK QUIET )
+IF( ITK_FOUND )
+    OPTION( OW_USE_ITK "Use the insight toolkit for image segmentation" OFF )
+    INCLUDE( ${ITK_USE_FILE} )
+    IF( OW_USE_ITK )
+        ADD_DEFINITIONS( -DOW_USE_ITK )
+    ENDIF()
+ENDIF()
+
+### Eigen #### (for the gauss process, the covariance matrices tend to be sparse and 20x20, but ~70.000 of them)
+FIND_PACKAGE( Eigen3 QUIET )
+IF( EIGEN3_FOUND )
+    MESSAGE( STATUS "Found Eigen3 in: ${EIGEN3_INCLUDE_DIR} with version: ${EIGEN3_VERSION}" )
+    MARK_AS_ADVANCED( EIGEN3_INCLUDE_DIR )
+    MARK_AS_ADVANCED( EIGEN3_VERSION )
+ENDIF()
+
+### OPENCL ###
+OPTION( OW_USE_OPENCL "Enable OpenCL if available." )
+IF( OW_USE_OPENCL )
+    FIND_PACKAGE( OpenCL QUIET )
+    IF( OPENCL_FOUND )
+        INCLUDE_DIRECTORIES( ${OPENCL_INCLUDE_DIR} )
+        INCLUDE_DIRECTORIES( ${OPENCL_CPP_INCLUDE_DIR} )
+        LINK_LIBRARIES( ${OPENCL_LIBRARY} )
+        MARK_AS_ADVANCED( OPENCL_INCLUDE_DIR )
+        MARK_AS_ADVANCED( OPENCL_LIBRARY )
+    ENDIF()
+ENDIF( OW_USE_OPENCL )
+
+### CUDA #### (e.g. for the detTractClustering module )
+OPTION( OW_USE_CUDA "Enable CUDA if available. Minimum version required is 2.3" )
+IF( OW_USE_CUDA )
+    FIND_PACKAGE( CUDA QUIET )
+    IF( CUDA_FOUND )
+        # BugFix: Subsequent calls don't set CUDA_VERSION_MAJOR or .._MINOR variables, so we have to extract them from CUDA_VERSION variable
+        STRING(REGEX REPLACE "([0-9]+)\\.([0-9]+).*" "\\1" CUDA_VERSION_MAJOR ${CUDA_VERSION})
+        STRING(REGEX REPLACE "([0-9]+)\\.([0-9]+).*" "\\2" CUDA_VERSION_MINOR ${CUDA_VERSION})
+
+        # Enforce at least CUDA version 2.3, since the detTractClustering is know to require this at least
+        SET( OW_MIN_CUDA_MAJOR_VERSION 2 )
+        SET( OW_MIN_CUDA_MINOR_VERSION 3 )
+
+        IF( CUDA_VERSION_MAJOR LESS OW_MIN_CUDA_MAJOR_VERSION )
+            SET( CUDA_FOUND_BUT_LOW_VERSION 1 )
+        ELSEIF( CUDA_VERSION_MAJOR EQUAL OW_MIN_CUDA_MAJOR_VERSION )
+            IF( CUDA_VERSION_MINOR LESS OW_MIN_CUDA_MINOR_VERSION )
+                SET( CUDA_FOUND_BUT_LOW_VERSION 1 )
+            ENDIF()
+        ENDIF()
+
+        # abort incase invalid version of CUDA was found.
+        IF( CUDA_FOUND_BUT_LOW_VERSION )
+            MESSAGE( FATAL_ERROR "You have selected to use CUDA but an insufficent version: ${CUDA_VERSION_MAJOR}.${CUDA_VERSION_MINOR} was found, but ${OW_MIN_CUDA_MAJOR_VERSION}.${OW_MIN_CUDA_MINOR_VERSION} is required." )
+        ENDIF()
+        MESSAGE( STATUS "CUDA version: ${CUDA_VERSION_MAJOR}.${CUDA_VERSION_MINOR} was found." )
+    ENDIF( CUDA_FOUND )
+ENDIF( OW_USE_CUDA )
+
+
 # other options:
 #---------------
 # Set default build type
@@ -122,6 +203,16 @@ IF( NOT CMAKE_BUILD_TYPE )
         FORCE
       )
 ENDIF( NOT CMAKE_BUILD_TYPE )
+
+# guard against typos in build-type strings
+STRING( TOLOWER "${CMAKE_BUILD_TYPE}" cmake_build_type_tolower)
+IF( NOT cmake_build_type_tolower STREQUAL "debug" AND
+    NOT cmake_build_type_tolower STREQUAL "release" AND
+    NOT cmake_build_type_tolower STREQUAL "relwithdebinfo" AND
+    NOT cmake_build_type_tolower STREQUAL "")
+  MESSAGE( SEND_ERROR "Unknown build type \"${CMAKE_BUILD_TYPE}\". Allowed values are Debug, Release, RelWithDebInfo  and \"\" (case-insensitive).")
+ENDIF()
+
 SET( EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}/bin CACHE PATH "The executables will be put into this directory." )
 MARK_AS_ADVANCED( LIBRARY_OUTPUT_PATH )
 MARK_AS_ADVANCED( EXECUTABLE_OUTPUT_PATH )
@@ -136,6 +227,8 @@ IF( CMAKE_GENERATOR MATCHES "Visual Studio" )
    SET( CMAKE_SHARED_LINKER_FLAGS " /STACK:10000000 /machine:I386 /NODEFAULTLIB:${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 /wd4101" )
+    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" )
@@ -167,24 +260,29 @@ ADD_SUBDIRECTORY( ext ) # The needed external libraries
 #-------------------------------------------------------------------------------------------------------------
 # Writes information about the revision of the current code to the file version.h which then gets included by OpenWalnut.cpp
 IF( NOT CMAKE_GENERATOR MATCHES "Visual Studio" )
-	add_custom_command( OUTPUT ${PROJECT_SOURCE_DIR}/version.h
-						MAIN_DEPENDENCY ${PROJECT_SOURCE_DIR}/../.hg/dirstate
-						COMMAND hg parents --template '\#define W_VERSION \"{node|short} {rev} {branches} {tags}\"' > ${PROJECT_SOURCE_DIR}/version.h
-						WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
-						COMMENT "Creating version.h"
-					 )
+    add_custom_command( OUTPUT ${PROJECT_SOURCE_DIR}/version.h
+                        MAIN_DEPENDENCY ${PROJECT_SOURCE_DIR}/../.hg/dirstate
+                        COMMAND hg parents --template '\#define W_VERSION \"{node|short} {rev} {branches} {tags}\" //' > ${PROJECT_SOURCE_DIR}/version.h
+                        WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
+                        COMMENT "Creating version.h"
+                     )
 ELSE()
-	add_custom_command( OUTPUT ${PROJECT_SOURCE_DIR}/version.h
-						MAIN_DEPENDENCY ${PROJECT_SOURCE_DIR}/../.hg/dirstate
-						COMMAND hg parents --template "\"#define W_VERSION \"\"{node|short} {rev} {branches} {tags}\"\"\"" > ${PROJECT_SOURCE_DIR}/version.h
-						WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
-						COMMENT "Creating version.h"
-					 )
+    add_custom_command( OUTPUT ${PROJECT_SOURCE_DIR}/version.h
+                        MAIN_DEPENDENCY ${PROJECT_SOURCE_DIR}/../.hg/dirstate
+                        COMMAND hg parents --template "\"#define W_VERSION \"\"{node|short} {rev} {branches} {tags}\"\"\"" > ${PROJECT_SOURCE_DIR}/version.h
+                        WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
+                        COMMENT "Creating version.h"
+                     )
 ENDIF()

 # finally, build walnut
 ADD_EXECUTABLE( walnut OpenWalnut.cpp version.h )
-TARGET_LINK_LIBRARIES( walnut OWkernel OWdataHandler OWgui OWguiqt4 OWcommon OWge ${Boost_LIBRARIES} )
+TARGET_LINK_LIBRARIES( walnut ${OWKernelName} ${OWDatahandlerName} ${OWguiName} ${OWguiqt4Name} ${OWCommonName} ${OWgeName} ${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 )
@@ -220,8 +318,8 @@ ENDIF()

 #---------- walnut.cfg file -------------
 IF( NOT EXISTS ${PROJECT_BINARY_DIR}/bin/${SHARED_FILES_RELATIVE}/walnut.cfg )
-  CONFIGURE_FILE( ${PROJECT_SOURCE_DIR}/../doc/user/walnut.cfg.mpi ${PROJECT_BINARY_DIR}/bin/${SHARED_FILES_RELATIVE}/walnut.cfg COPYONLY )
-  MESSAGE( STATUS "Copied ${PROJECT_SOURCE_DIR}/../doc/user/walnut.cfg.mpi to ${PROJECT_BINARY_DIR}/bin/${SHARED_FILES_RELATIVE}/walnut.cfg" )
+  CONFIGURE_FILE( ${PROJECT_SOURCE_DIR}/../doc/user/walnut.cfg.official ${PROJECT_BINARY_DIR}/bin/${SHARED_FILES_RELATIVE}/walnut.cfg COPYONLY )
+  MESSAGE( STATUS "Copied ${PROJECT_SOURCE_DIR}/../doc/user/walnut.cfg.official to ${PROJECT_BINARY_DIR}/bin/${SHARED_FILES_RELATIVE}/walnut.cfg" )
 ENDIF()

 # Special targets:
@@ -267,15 +365,17 @@ ADD_CUSTOM_TARGET( tags DEPENDS ctags DEPENDS cscope )

 #-------------------------------------------------------------------------------------------------------------
 # Determines the number of cores available on this machine
-SET( NUM_CORES_SOURCE_DIR ${PROJECT_SOURCE_DIR}/../tools/numCores )
-SET( NUM_CORES_BINARY_DIR ${PROJECT_BINARY_DIR}/numCores )
-SET( NUM_CORES_BINARY ${NUM_CORES_BINARY_DIR}/numCores )
-ADD_CUSTOM_TARGET( numCores
+IF( NOT CMAKE_GENERATOR MATCHES "Visual Studio" )
+    SET( NUM_CORES_SOURCE_DIR ${PROJECT_SOURCE_DIR}/../tools/numCores )
+    SET( NUM_CORES_BINARY_DIR ${PROJECT_BINARY_DIR}/numCores )
+    SET( NUM_CORES_BINARY ${NUM_CORES_BINARY_DIR}/numCores )
+    ADD_CUSTOM_TARGET( numCores
                   COMMAND ${CMAKE_COMMAND} -E make_directory ${NUM_CORES_BINARY_DIR}
                   COMMAND cd ${NUM_CORES_BINARY_DIR} && ${CMAKE_COMMAND} ${NUM_CORES_SOURCE_DIR} > /dev/null
                   COMMAND $(MAKE) -C ${NUM_CORES_BINARY_DIR} > /dev/null
                   COMMENT "Determines the number of cores available on this machine"
                 )
+ENDIF()

 #-------------------------------------------------------------------------------------------------------------
 # Checks style guide lines via the BrainLint tool against all source code files
@@ -283,6 +383,7 @@ ADD_CUSTOM_TARGET( numCores
 #    noncolored if it is set to OFF
 FILE( GLOB_RECURSE STYLE_CPP ${PROJECT_SOURCE_DIR}/*.cpp )
 FILE( GLOB_RECURSE STYLE_H ${PROJECT_SOURCE_DIR}/*.h )
+FILE( GLOB_RECURSE STYLE_GLSL ${PROJECT_SOURCE_DIR}/*.glsl )
 # Set dirs to exclude from stylecheck
 SET( EXCLUDE_DIRS "/ext/nifti/;/dataHandler/io/biosig/;/dataHandler/io/biosigWin/;/dataHandler/io/biosig/XMLParser/;/dataHandler/io/biosigWin/XMLParser/;/ext/libeep/avr/;/ext/libeep/cnt/;/ext/libeep/eep/;/common/platformDependent/visualStudio/;/modules/lic/fibernavigator/;/modules/lic/fantom/" )
 FOREACH( dirname ${EXCLUDE_DIRS} )
@@ -314,7 +415,7 @@ ELSE()
 ENDIF()

 FILE( WRITE ${PROJECT_BINARY_DIR}/brainlintlist "" )
-FOREACH( fname ${STYLE_CPP} ${STYLE_H} )
+FOREACH( fname ${STYLE_CPP} ${STYLE_H} ${STYLE_GLSL} )
    FILE( APPEND ${PROJECT_BINARY_DIR}/brainlintlist "${fname}\n" )
 ENDFOREACH()

@@ -325,7 +426,25 @@ ADD_CUSTOM_TARGET( stylecheck
                   COMMENT "Check if code complies to CodingStandard"
                 )

+
+#-------------------------------------------------------------------------------------------------------------
+# Removes nasty windows line endings
+ADD_CUSTOM_TARGET( removewinlineendings
+                   COMMAND ${PYTHON_EXECUTABLE} ${PROJECT_SOURCE_DIR}/../tools/removeWinLineEnding.py ${PROJECT_BINARY_DIR}/brainlintlist
+                   WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
+                   COMMENT "Removes Windows Line endings"
+                 )
+
 #-------------------------------------------------------------------------------------------------------------
+# windows helper script to copy all files needed to build a release to one folder
+IF( CMAKE_GENERATOR MATCHES "Visual Studio" )
+    ADD_CUSTOM_TARGET( copyWinRelease
+                       COMMAND ${PYTHON_EXECUTABLE} ${PROJECT_SOURCE_DIR}/../tools/copyWinRelease.py
+                       WORKING_DIRECTORY ${PROJECT_BINARY_DIR}
+                       COMMENT "Copys all the necessary Windows dll's and executables so binaries can easyly be distributed"
+                     )
+ENDIF( CMAKE_GENERATOR MATCHES "Visual Studio" )
+                 #-------------------------------------------------------------------------------------------------------------
 # Prints the verbose output of the test runners, so you may identify the source of error early, if any
 ADD_CUSTOM_TARGET( vtest
                   COMMAND $(MAKE) test ARGS="-V"

--- a/src/OpenWalnut.cpp
+++ b/src/OpenWalnut.cpp
@@ -36,6 +36,10 @@
 * \par
 * http://www.openwalnut.org
 * \par
+ * There exist two versions of this API.
+ * A simple one at http://berkeley.informatik.uni-leipzig.de/api/
+ * and one with callgraphs at http://berkeley.informatik.uni-leipzig.de/apiFull/
+ * \par
 * Copyright 2009-2010 OpenWalnut Community, BSV\@Uni-Leipzig and CNCF\@MPI-CBS.
 * For more information see http://www.openwalnut.org/copying
 */
@@ -59,20 +63,14 @@ int main( int argc, char** argv )
    // install signal handler as early as possible
    WSegmentationFault::installSignalHandler();

-    // init logger here. It will be started by the GUI.
-    WLogger logger;
+    // initialize logger here. It will be started by the GUI.
+    WLogger::startup();

    // initialize GUI
-    // NOTE: we need a shared ptr here since WGUI uses enable_shared_from_this.
+    // NOTE: we need a shared_ptr here since WGUI uses enable_shared_from_this.
    boost::shared_ptr< WQt4Gui > gui = boost::shared_ptr< WQt4Gui > ( new WQt4Gui( argc, argv ) );
    int result = gui->run();

-    // finish running thread if there is a WLogger.
-    if( !result )
-    {
-        WLogger::getLogger()->wait( true );
-    }
-
    std::cout << "Closed OpenWalnut smoothly. Goodbye!" << std::endl;

    return result;

--- a/src/README
+++ b/src/README
@@ -6,6 +6,6 @@ Directory Structure:
    -gui
    -dataHandler
    -graphicsEngine
-    -math
    -common
    -kernel
+    -tools
--- a/src/common/CMakeLists.txt
+++ b/src/common/CMakeLists.txt
@@ -7,24 +7,45 @@ ADD_SUBDIRECTORY( datastructures )
 ADD_SUBDIRECTORY( constraints )
 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} ${CMAKE_DL_LIBS} )
+SET( LIB_NAME "${OWCommonName}" )
+
+SET( ${LIB_NAME}_COMBINER_SRC ${COMMON_SRC} ${COMMON_DATASTRUCTURES_SRC} ${COMMON_EXCEPTIONS_SRC} ${MATH_SRC} )
+SET( ${LIB_NAME}_ALL_CPP ${COMMON_SRC} ${COMMON_DATASTRUCTURES_SRC} ${COMMON_EXCEPTIONS_SRC} ${MATH_SRC}  )
+FILE( GLOB_RECURSE ${LIB_NAME}_REMOVE_H "*.h"  )
+
+LIST( REMOVE_ITEM ${LIB_NAME}_ALL_CPP ${${LIB_NAME}_REMOVE_H} )
+
+IF( OW_BUILD_AS_ONE_BIG_FILE )
+	SET( UNITY_BUILD_FILE_NAME "${LIB_NAME}UnityBuildFile.cpp" )
+	GENERATE_UNITY_BUILD_FILE( ${LIB_NAME}_ALL_CPP )
+	ADD_LIBRARY( ${LIB_NAME} SHARED ${UNITY_BUILD_FILE_NAME} ${${LIB_NAME}_COMBINER_SRC} )
+ENDIF( OW_BUILD_AS_ONE_BIG_FILE )
+
+IF( NOT OW_BUILD_AS_ONE_BIG_FILE )
+    ADD_LIBRARY( ${LIB_NAME} SHARED ${${LIB_NAME}_COMBINER_SRC} )
+ENDIF( NOT OW_BUILD_AS_ONE_BIG_FILE )
+
+TARGET_LINK_LIBRARIES( ${LIB_NAME} ${Boost_LIBRARIES} ${CMAKE_DL_LIBS} ${OPENSCENEGRAPH_LIBRARIES} )
+
+IF(MSVC_IDE)
+    SET_TARGET_PROPERTIES( ${LIB_NAME} 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
-# the quotes on the command line. WSharedLib::getSystemPrefix and 
+# the quotes on the command line. WSharedLib::getSystemPrefix and
 # getSystemSuffix hard codes the right strings for VC.
 # Maybe you have to spend another 500 bucks to have your VC support quotes.
 IF( NOT CMAKE_GENERATOR MATCHES "Visual Studio" )
-	add_definitions( '-DW_LIB_PREFIX="${CMAKE_SHARED_LIBRARY_PREFIX}"' )
-	add_definitions( '-DW_LIB_SUFFIX="${CMAKE_SHARED_LIBRARY_SUFFIX}"' )
+    add_definitions( '-DW_LIB_PREFIX="${CMAKE_SHARED_LIBRARY_PREFIX}"' )
+    add_definitions( '-DW_LIB_SUFFIX="${CMAKE_SHARED_LIBRARY_SUFFIX}"' )
 ENDIF()

 # Unit tests
 IF( OW_COMPILE_TESTS )
  CXXTEST_ADD_TESTS_FROM_LIST( "${COMMON_SRC}"
-                               "OWcommon"
+                               "${LIB_NAME}"
                               "WSegmentationFault.cpp" # can't test seg-faults ;-)
                               "WTransferable.cpp"  # its an empty class
                               "WPropertyBase.cpp" # its an abstract class. Its small functionality is tested in WPropertyVariable_test.h

--- a/src/common/WBoundingBox.cpp
+++ b/src/common/WBoundingBox.cpp
+//---------------------------------------------------------------------------
+//
+// Project: OpenWalnut ( http://www.openwalnut.org )
+//
+// Copyright 2009 OpenWalnut Community, BSV@Uni-Leipzig and CNCF@MPI-CBS
+// For more information see http://www.openwalnut.org/copying
+//
+// This file is part of OpenWalnut.
+//
+// OpenWalnut is free software: you can redistribute it and/or modify
+// it under the terms of the GNU Lesser General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// OpenWalnut is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with OpenWalnut. If not, see <http://www.gnu.org/licenses/>.
+//
+//---------------------------------------------------------------------------
+
+#include "WBoundingBox.h"
+
+
--- a/src/common/WBoundingBox.h
+++ b/src/common/WBoundingBox.h