[MERGE] - merged in 1.2.5 release branch

doc/qt4gui/help/OpenWalnutWelcome.html

-<h1>Welcome to OpenWalnut %OW_LIB_VERSION%!</h1>
+<h1>Welcome to OpenWalnut %OW_LIB_VERSION% Developmet Version!</h1>
 <a href="http://www.openwalnut.org/projects/openwalnut/wiki/ReleaseNotes">Release Notes</a>
 <br>
 <br>

resources/core-dev/lib/pkgconfig/openwalnut.pc

+prefix=@CMAKE_INSTALL_PREFIX@
+exec_prefix=${prefix}
+includedir=${prefix}/include
+libdir=${exec_prefix}/lib
+
+Name: openwalnut
+Description: The OpenWalnut core library -- OpenWalnut is a tool for multi-modal medical and brain data visualization.
+Version: 1.2.5
+Cflags: -I${includedir}/openwalnut @EIGEN3_DEFINES@
+Libs: -L${libdir} -lopenwalnut
+Requires: openscenegraph eigen3

src/CMakeLists.txt

@@ -142,7 +142,8 @@ SET( CMAKE_CXX_FLAGS_RELWITHDEBINFO "-g -DDEBUG -O2" CACHE STRING "" FORCE )
 # Eigen3 specifics
 
 # NOTE: this is included in ext. But we need to set several definitions to make this work on 32 Bit machines due to alignment problems
-ADD_DEFINITIONS( -DEIGEN_DONT_VECTORIZE -DEIGEN_DONT_ALIGN -DEIGEN_DISABLE_UNALIGNED_ARRAY_ASSERT )
+SET( EIGEN3_DEFINES -DEIGEN_DONT_VECTORIZE -DEIGEN_DONT_ALIGN -DEIGEN_DISABLE_UNALIGNED_ARRAY_ASSERT )
+ADD_DEFINITIONS( ${EIGEN3_DEFINES} )
 
 # ---------------------------------------------------------------------------------------------------------------------------------------------------
 #

src/core/CMakeLists.txt

@@ -68,6 +68,9 @@ SETUP_LIB_INSTALL( ${LibName} ${OW_LIBRARY_DIR_RELATIVE} "CORE" )
 # NOTE: do not use ${TARGET_H_FILES}. The command requires a list
 SETUP_DEV_INSTALL( ${LibName} ${OW_LIBRARY_DIR_RELATIVE} TARGET_H_FILES "include/openwalnut/core" "CORE_DEV" )
 
+# The core does also provide some nice pkg-config file. Set this up and configure it to contain the correct install prefix
+SETUP_CONFIGURED_FILE( "core-dev" "lib/pkgconfig/openwalnut.pc" "CORE_DEV" )
+
 # ---------------------------------------------------------------------------------------------------------------------------------------------------
 # Test Setup
 # ---------------------------------------------------------------------------------------------------------------------------------------------------

src/core/dataHandler/WDataSetDTI.h

@@ -51,7 +51,7 @@ public:
     ~WDataSetDTI();
 
     /**
-     * Creates a copy (clone) of this instance but allows to change the valueset. Unlike copy construction, this is a very useful function if you
+     * Creates a copy (clone) of this instance but allows one to change the valueset. Unlike copy construction, this is a very useful function if you
      * want to keep the dynamic type of your dataset even if you just have a WDataSetSingle.
      *
      * \param newValueSet the new valueset.
@@ -61,7 +61,7 @@ public:
     virtual WDataSetSingle::SPtr clone( boost::shared_ptr< WValueSetBase > newValueSet ) const;
 
     /**
-     * Creates a copy (clone) of this instance but allows to change the grid. Unlike copy construction, this is a very useful function if you
+     * Creates a copy (clone) of this instance but allows one to change the grid. Unlike copy construction, this is a very useful function if you
      * want to keep the dynamic type of your dataset even if you just have a WDataSetSingle.
      *
      * \param newGrid the new grid.

src/core/dataHandler/WDataSetRawHARDI.h

@@ -67,7 +67,7 @@ public:
     virtual ~WDataSetRawHARDI();
 
     /**
-     * Creates a copy (clone) of this instance but allows to change the valueset. Unlike copy construction, this is a very useful function if you
+     * Creates a copy (clone) of this instance but allows one to change the valueset. Unlike copy construction, this is a very useful function if you
      * want to keep the dynamic type of your dataset even if you just have a WDataSetSingle.
      *
      * \param newValueSet the new valueset.
@@ -77,7 +77,7 @@ public:
     virtual WDataSetSingle::SPtr clone( boost::shared_ptr< WValueSetBase > newValueSet ) const;
 
     /**
-     * Creates a copy (clone) of this instance but allows to change the grid. Unlike copy construction, this is a very useful function if you
+     * Creates a copy (clone) of this instance but allows one to change the grid. Unlike copy construction, this is a very useful function if you
      * want to keep the dynamic type of your dataset even if you just have a WDataSetSingle.
      *
      * \param newGrid the new grid.

src/core/dataHandler/WDataSetScalar.h

@@ -63,7 +63,7 @@ public:
     virtual ~WDataSetScalar();
 
     /**
-     * Creates a copy (clone) of this instance but allows to change the valueset. Unlike copy construction, this is a very useful function if you
+     * Creates a copy (clone) of this instance but allows one to change the valueset. Unlike copy construction, this is a very useful function if you
      * want to keep the dynamic type of your dataset even if you just have a WDataSetSingle.
      *
      * \param newValueSet the new valueset.
@@ -73,7 +73,7 @@ public:
     virtual WDataSetSingle::SPtr clone( boost::shared_ptr< WValueSetBase > newValueSet ) const;
 
     /**
-     * Creates a copy (clone) of this instance but allows to change the grid. Unlike copy construction, this is a very useful function if you
+     * Creates a copy (clone) of this instance but allows one to change the grid. Unlike copy construction, this is a very useful function if you
      * want to keep the dynamic type of your dataset even if you just have a WDataSetSingle.
      *
      * \param newGrid the new grid.

src/core/dataHandler/WDataSetSegmentation.h

@@ -123,7 +123,7 @@ public:
     virtual const std::string getDescription() const;
 
     /**
-     * Creates a copy (clone) of this instance but allows to change the valueset. Unlike copy construction, this is a very useful function if you
+     * Creates a copy (clone) of this instance but allows one to change the valueset. Unlike copy construction, this is a very useful function if you
      * want to keep the dynamic type of your dataset even if you just have a WDataSetSingle.
      *
      * \param newValueSet the new valueset.
@@ -133,7 +133,7 @@ public:
     virtual WDataSetSingle::SPtr clone( boost::shared_ptr< WValueSetBase > newValueSet ) const;
 
     /**
-     * Creates a copy (clone) of this instance but allows to change the grid. Unlike copy construction, this is a very useful function if you
+     * Creates a copy (clone) of this instance but allows one to change the grid. Unlike copy construction, this is a very useful function if you
      * want to keep the dynamic type of your dataset even if you just have a WDataSetSingle.
      *
      * \param newGrid the new grid.
@@ -179,7 +179,7 @@ protected:
 
 private:
     /**
-     * This helper function converts the probabilities given by three seperate WDataSetScalars to one WValueSetBase.
+     * This helper function converts the probabilities given by three separate WDataSetScalars to one WValueSetBase.
      *
      * \param whiteMatter the probabilities for white matter.
      * \param grayMatter the probabilities for gray matter.

src/core/dataHandler/WDataSetSingle.h

@@ -78,7 +78,7 @@ public:
     virtual ~WDataSetSingle();
 
     /**
-     * Creates a copy (clone) of this instance but allows to change the valueset. Unlike copy construction, this is a very useful function if you
+     * Creates a copy (clone) of this instance but allows one to change the valueset. Unlike copy construction, this is a very useful function if you
      * want to keep the dynamic type of your dataset even if you just have a WDataSetSingle.
      *
      * \param newValueSet the new valueset.
@@ -88,7 +88,7 @@ public:
     virtual WDataSetSingle::SPtr clone( boost::shared_ptr< WValueSetBase > newValueSet ) const;
 
     /**
-     * Creates a copy (clone) of this instance but allows to change the grid. Unlike copy construction, this is a very useful function if you
+     * Creates a copy (clone) of this instance but allows one to change the grid. Unlike copy construction, this is a very useful function if you
      * want to keep the dynamic type of your dataset even if you just have a WDataSetSingle.
      *
      * \param newGrid the new grid.

src/core/dataHandler/WDataSetSphericalHarmonics.h

@@ -63,7 +63,7 @@ public:
     virtual ~WDataSetSphericalHarmonics();
 
     /**
-     * Creates a copy (clone) of this instance but allows to change the valueset. Unlike copy construction, this is a very useful function if you
+     * Creates a copy (clone) of this instance but allows one to change the valueset. Unlike copy construction, this is a very useful function if you
      * want to keep the dynamic type of your dataset even if you just have a WDataSetSingle.
      *
      * \param newValueSet the new valueset.
@@ -73,7 +73,7 @@ public:
     virtual WDataSetSingle::SPtr clone( boost::shared_ptr< WValueSetBase > newValueSet ) const;
 
     /**
-     * Creates a copy (clone) of this instance but allows to change the grid. Unlike copy construction, this is a very useful function if you
+     * Creates a copy (clone) of this instance but allows one to change the grid. Unlike copy construction, this is a very useful function if you
      * want to keep the dynamic type of your dataset even if you just have a WDataSetSingle.
      *
      * \param newGrid the new grid.

src/core/dataHandler/WDataSetVector.h

@@ -56,7 +56,7 @@ public:
     virtual ~WDataSetVector();
 
     /**
-     * Creates a copy (clone) of this instance but allows to change the valueset. Unlike copy construction, this is a very useful function if you
+     * Creates a copy (clone) of this instance but allows one to change the valueset. Unlike copy construction, this is a very useful function if you
      * want to keep the dynamic type of your dataset even if you just have a WDataSetSingle.
      *
      * \param newValueSet the new valueset.
@@ -66,7 +66,7 @@ public:
     virtual WDataSetSingle::SPtr clone( boost::shared_ptr< WValueSetBase > newValueSet ) const;
 
     /**
-     * Creates a copy (clone) of this instance but allows to change the grid. Unlike copy construction, this is a very useful function if you
+     * Creates a copy (clone) of this instance but allows one to change the grid. Unlike copy construction, this is a very useful function if you
      * want to keep the dynamic type of your dataset even if you just have a WDataSetSingle.
      *
      * \param newGrid the new grid.

src/core/dataHandler/WSubject.h

@@ -85,7 +85,7 @@ public:
     WSubject();
 
     /**
-     * Allows to give the subject information the person during construction.
+     * Allows one to give the subject information the person during construction.
      *
      * \param personInfo personal information object
      */

src/modules/HARDIToSphericalHarmonics/WMHARDIToSphericalHarmonics.cpp

@@ -256,7 +256,7 @@ void WMHARDIToSphericalHarmonics::properties()
                                                       m_propCondition );
 
     m_doResidualCalculation = m_properties->addProperty( "Residual Calculation",
-                                                         "Indicating whether the reprojection errors is stored into a seperate dataset.",
+                                                         "Indicating whether the reprojection errors is stored into a separate dataset.",
                                                          false,
                                                          m_propCondition );
 

src/modules/HARDIToSphericalHarmonics/WMHARDIToSphericalHarmonics.h

@@ -126,7 +126,7 @@ private:
     WPropBool m_doErrorCalculation; //!< Property indicating whether a reprojection error of the spherical harmonics is calculated.
 
     /**
-     * Property indicating whether the reprojection error (measurement relative to spherical harmonic calculation) is stored into a seperate dataset.
+     * Property indicating whether the reprojection error (measurement relative to spherical harmonic calculation) is stored into a separate dataset.
      */
     WPropBool m_doResidualCalculation;
 

src/modules/atlasCreator/WMAtlasCreator.h

@@ -111,7 +111,7 @@ private:
     /**
      * loads and parses the meta file
      * \param path to the meta file
-     * \return true if a meta file was succesfully loaded, false otherwise
+     * \return true if a meta file was successfully loaded, false otherwise
      */
     bool loadPngs( boost::filesystem::path path );
 

src/modules/atlasSurfaces/WMAtlasSurfaces.cpp

@@ -90,7 +90,7 @@ const std::string WMAtlasSurfaces::getName() const
 const std::string WMAtlasSurfaces::getDescription() const
 {
     return "Use a scalar data set that stores numbers for atlas regions and a "
-        "correspoding text file with labels for the numbers to create "
+        "corresponding text file with labels for the numbers to create "
         "surfaces bounding the atlas regions. The surfaces can be picked to reveal "
         "their name in the HUD (module). Regions can be used as ROIs for fiber selection.";
 }

src/modules/clusterDisplayVoxels/WMClusterDisplayVoxels.h

@@ -60,7 +60,7 @@ typedef enum
 CDV_DISPLAYMODE;
 
 /**
- * Allows to display and interact with clustered voxel data.
+ * Allows one to display and interact with clustered voxel data.
  * \ingroup modules
  */
 class WMClusterDisplayVoxels: public WModule
@@ -125,7 +125,7 @@ private:
     /**
      * loads and parses the clustering text file
      * \param clusterFile to the clustering file
-     * \return true if a meta file was succesfully loaded, false otherwise
+     * \return true if a meta file was successfully loaded, false otherwise
      */
     bool loadClustering( boost::filesystem::path clusterFile );
 

src/modules/data/WMWriteNIfTI.h

@@ -106,7 +106,7 @@ protected:
 
 private:
     /**
-     * Allows to get a void* out of WValueSet.
+     * Allows one to get a void* out of WValueSet.
      * \param returnData the casted data will be returned through this pointer.
      */
     template< typename T > void castData( void*& returnData );

src/modules/data/ext/libeep/libcnt/cnt.c

@@ -2330,7 +2330,7 @@ int eep_has_recording_info(eeg_t *cnt)
 
 void eep_set_recording_info(eeg_t *cnt, record_info_t* info)
 {
-/* previous: 
+/* previous:
   if (NULL != cnt->recording_info)
   v_free(cnt->recording_info);
   cnt->recording_info = (record_info_t*) v_malloc(sizeof(record_info_t) , "recording_info");
@@ -2603,7 +2603,7 @@ void eep_get_dataformat(eeg_t *cnt, char *format)
       strcpy(format, "EEP 2.0 (16 bit channel multiplexed)"); break;
     case CNT_RIFF:
       if( eep_get_fileversion_major(cnt) )
-        sprintf(format, "EEP %d.%d", eep_get_fileversion_major(cnt), eep_get_fileversion_minor(cnt));  
+        sprintf(format, "EEP %d.%d", eep_get_fileversion_major(cnt), eep_get_fileversion_minor(cnt));
       else
         sprintf(format, "EEP 3.x");
       if( eep_has_data_of_type(cnt, DATATYPE_EEG) )
@@ -2614,8 +2614,8 @@ void eep_get_dataformat(eeg_t *cnt, char *format)
         strcat(format, " average");
       if( eep_has_data_of_type(cnt, DATATYPE_STDDEV) )
         strcat(format, " stddev");
-      if( eep_has_data_of_type(cnt, DATATYPE_TIMEFREQ) || 
-          eep_has_data_of_type(cnt, DATATYPE_AVERAGE)  || 
+      if( eep_has_data_of_type(cnt, DATATYPE_TIMEFREQ) ||
+          eep_has_data_of_type(cnt, DATATYPE_AVERAGE)  ||
           eep_has_data_of_type(cnt, DATATYPE_STDDEV) )
         strcat(format, " (float vectors)");
       break;
@@ -2662,14 +2662,14 @@ int eep_read_float(eeg_t *cnt, eep_datatype_e type, float *muxbuf, slen_t n)
 
   if (CNT_RIFF != cnt->mode && CNT_AVR != cnt->mode)
     return CNTERR_BADREQ;
-  
+
   if (!store->initialized)
     return CNTERR_DATA; /* No such data in this file */
- 
+
   if (store->data.readpos + store->data.bufepoch * store->epochs.epochl +
       n > (DATATYPE_TIMEFREQ == type ? eep_get_tf_samplec(cnt) : eep_get_samplec(cnt)))
     return CNTERR_RANGE;
-  
+
   switch (type)
   {
     case DATATYPE_TIMEFREQ:
@@ -2800,10 +2800,10 @@ void eep_set_pre_stimulus_interval(eeg_t *cnt, double pre_stimulus)
 
 /*****************************************************************************/
 /*********************** Recording time/date routines ************************/
-/* 
+/*
  some info:
  please visit http://www.minelinks.com/calendar_converter.html for more information
- the offset(diff between 1jan1970 and 30dec1899) is 2209161600( 70 years in seconds) 
+ the offset(diff between 1jan1970 and 30dec1899) is 2209161600( 70 years in seconds)
  *****************************************************************************/
 
 void
@@ -2824,7 +2824,7 @@ eep_unixdate_to_exceldate(time_t epoch, double *excel, double *fraction) {
   double return_value=0;
 
   return_value=(double)(epoch + 2209161600) / (3600.0*24.0);
-  
+
   (*excel) = return_value;
   (*fraction) = 0;
 }
@@ -3237,7 +3237,7 @@ int trg_read_NS30(eeg_t *EEG)
             rsshift = (slen_t) (0.08 / EEG->eep_header.period + 0.5);
       break;
 
-    default: eeperror("unknonw NS cnt type (%d)\n", EEG->ns_cnttype);
+    default: eeperror("unknown NS cnt type (%d)\n", EEG->ns_cnttype);
   }
 
 

src/modules/data/io/WReaderNIfTI.h

@@ -88,7 +88,7 @@ public:
 protected:
 private:
     /**
-     * This function allows to copy the data given as a T*
+     * This function allows one to copy the data given as a T*
      * by niftilibio into a std::vector< T >
      * \param dataArray data to copy
      * \param countVoxels number of voxels stored in dataArray