Merge with 27859cd196294dd78293ecddf497ee2103d110df

src/common/WColor.h

@@ -25,9 +25,9 @@
 #ifndef WCOLOR_H
 #define WCOLOR_H
 
+#include <cassert>
 #include <istream>
 #include <ostream>
-#include <cassert>
 #include <string>
 #include <vector>
 
@@ -104,13 +104,20 @@ public:
 
 protected:
 private:
-    float m_red;
-    float m_green;
-    float m_blue;
-    float m_alpha;
+    float m_red; //!< Red channel
+    float m_green; //!< Green channel
+    float m_blue; //!< Blue channel
+    float m_alpha; //!< Alpha channel
 };
 
+/**
+ * Write a color in string represensation to the given output stream.
+ */
 std::ostream& operator<<( std::ostream& out, const WColor& c );
+
+/**
+ * Write a color in string represensation to the given input stream.
+ */
 std::istream& operator>>( std::istream& in, WColor& c );
 
 #endif  // WCOLOR_H

src/common/WLogger.h

@@ -27,6 +27,7 @@
 
 #include <queue>
 #include <string>
+#include <sstream>
 #include <vector>
 
 #include <boost/shared_ptr.hpp>
@@ -209,4 +210,164 @@ private:
     std::string m_defaultFileFormat;
 };
 
+/**
+ * This namespace collects several convinient access points such as wlog::err
+ * for logging with streams to our WLogger.
+ */
+namespace wlog
+{
+/**
+ * Resource class for streamed logging.
+ */
+class WStreamedLogger
+{
+public:
+    /**
+     * Creates new streamed logger instance. Logging is deferred until
+     * destruction of this instance.
+     *
+     * \param source Source from which the log message originates
+     * \param level The LogLevel of the message
+     */
+    WStreamedLogger( const std::string& source, LogLevel level );
+
+    /**
+     * Appends something loggable (to std::string castable) to the log.
+     */
+    template< typename T > WStreamedLogger operator<<( const T& loggable );
+
+    // alias for std::endl etc. type
+    typedef std::basic_ostream< char, std::char_traits< char > > OutStreamType;
+    typedef OutStreamType& ( *StreamManipulatorFunctor )( OutStreamType& );
+
+    /**
+     * This is totally crazy man! Don't get dizzy on that, watch out and 
+     * ask a C++ guru next to your side, which is probably named Christian
+     * or have a look on that: http://stackoverflow.com/questions/1134388/stdendl-is-of-unknown-type-when-overloading-operator
+     *
+     * Allow std::endl to be streamed into log messages.
+     *
+     * \param manip Function pointer e.g. std::endl, std::flush, std::ends
+     * \return The streamed logger for further use
+     */
+    WStreamedLogger operator<<( StreamManipulatorFunctor manip );
+
+protected:
+private:
+    /**
+     * Actually implementing the streaming functionality.
+     */
+    class Buffer
+    {
+    public: // NOLINT inner classes may have also lables
+        /**
+         * Constructs a new stream for logging.
+         *
+         * \param source String identifying the source of the message
+         * \param level LogLevel of the message
+         */
+        Buffer( const std::string& source, LogLevel level );
+
+        /**
+         * Commits the logging expression to our WLogger
+         */
+        virtual ~Buffer();
+
+        std::ostringstream m_logString; //!< queuing up parts of the log message
+        LogLevel m_level; //!< Default logging level for this stream
+        std::string m_source; //!< The source of the logging message
+    };
+
+    /**
+     * Forbid assignment
+     *
+     * \param rhs The instance which SHOULD be copied over
+     */
+    WStreamedLogger& operator=( const WStreamedLogger& rhs );
+
+    boost::shared_ptr< Buffer > m_buffer; //!< Collects the message parts.
+};
+
+inline WStreamedLogger::WStreamedLogger( const std::string& source, LogLevel level )
+    : m_buffer( new Buffer( source, level ) )
+{
+}
+
+template< typename T > inline WStreamedLogger WStreamedLogger::operator<<( const T& loggable )
+{
+    m_buffer->m_logString << loggable;
+    return *this;
+}
+
+inline WStreamedLogger WStreamedLogger::operator<<( StreamManipulatorFunctor manip )
+{
+    manip( m_buffer->m_logString );
+    return *this;
+}
+
+inline WStreamedLogger::Buffer::~Buffer()
+{
+    WLogger::getLogger()->addLogMessage( m_logString.str(), m_source, m_level );
+}
+
+inline WStreamedLogger::Buffer::Buffer( const std::string& source, LogLevel level )
+    : m_logString(),
+      m_level( level ),
+      m_source( source )
+{
+}
+
+/**
+ * Convinient function for logging messages to our WLogger but not for
+ * public use outside of this module.
+ *
+ * \param source Indicate the source where this log message origins.
+ * \param level The LogLevel of this message
+ */
+inline WStreamedLogger _wlog( const std::string& source, LogLevel level )
+{
+    return WStreamedLogger( source, level );
+}
+
+/**
+ * Logging an error message.
+ *
+ * \param source Indicate the source where this log message origins.
+ */
+inline WStreamedLogger error( const std::string& source )
+{
+    return _wlog( source, LL_ERROR );
+}
+
+/**
+ * Loggin a warning message.
+ *
+ * \param source Indicate the source where this log message origins.
+ */
+inline WStreamedLogger warn( const std::string& source )
+{
+    return _wlog( source, LL_WARNING );
+}
+
+/**
+ * Loggin an information message.
+ *
+ * \param source Indicate the source where this log message origins.
+ */
+inline WStreamedLogger info( const std::string& source )
+{
+    return _wlog( source, LL_INFO );
+}
+
+/**
+ * Loggin a debug message.
+ *
+ * \param source Indicate the source where this log message origins.
+ */
+inline WStreamedLogger debug( const std::string& source )
+{
+    return _wlog( source, LL_DEBUG );
+}
+} // end of namespace log
+
 #endif  // WLOGGER_H

src/common/WStatusReport.h

@@ -38,6 +38,8 @@ public:
     /**
      * Constructs a new status reporter with the number of total steps
      * which it should reach to reach the 100 percent.
+     *
+     * \param totalSteps Number of total steps which symbolize 100 percent.
      */
     explicit WStatusReport( unsigned int totalSteps );
 
@@ -65,14 +67,16 @@ public:
     /**
      * Increments the finished work by the number of the given steps.
      *
+     * \param numSteps Number of steps to increment
      * \return The progress()
      */
     double operator+=( unsigned int numSteps );
 
     /**
-     * Generates a string which represents the progress in terms of
-     * characters. When reaching 100 percent finally finalNumOfSymbols are
-     * returned.
+     * Generates a string which represents the progress as bar of chars.
+     *
+     * \param symbol The char used for the progressbar indication
+     * \param finalNumOfSymbols How many symbols represent the 100 percent
      */
     std::string stringBar( char symbol = '#', unsigned int finalNumOfSymbols = 50 ) const;
 
@@ -82,5 +86,4 @@ private:
     unsigned int m_finishedSteps; //!< indicates the work done so far
 };
 
-
 #endif  // WSTATUSREPORT_H

src/dataHandler/io/WIOTools.hpp

@@ -56,6 +56,8 @@ namespace wiotools
 
     /**
      * Transforms a value of type T into the opposite byte order.
+     *
+     * \param value The value where byte swapping should be applied to
      */
     template< class T > T switchByteOrder( const T value )
     {
@@ -77,6 +79,10 @@ namespace wiotools
     /**
      * Transform a whole array of elements (of type T and size of sizeof(T))
      * into opposite byte order.
+     *
+     * \param array Array containing the data
+     * \param arraySize The number of elements which is not the number of
+     * bytes but e.g. the number of floats
      */
     template< class T > void switchByteOrderOfArray( T *array, const size_t arraySize )
     {
@@ -87,6 +93,7 @@ namespace wiotools
     }
 
     /**
+     * \param name File name to get the extension or suffix from.
      * \return filename suffix
      */
     inline std::string getSuffix( std::string name )
@@ -96,17 +103,23 @@ namespace wiotools
 
     /**
      * Checks if a given path already exists or not
+     *
+     * \param path Path to be checked on existence
      */
     inline bool fileExists( std::string path )
     {
         return boost::filesystem::exists( boost::filesystem::path( path ) );
     }
 
+    /**
+     * Generate a file name with full path for a temp file. Watch out on all
+     * platforms!
+     */
     inline std::string tempFileName()
     {
         // REGARDING THE COMPILER WARNING
         // 1. mkstemp is only available for POSIX systems
-        // 2. the warning generated here is due to a race condition
+        // 2. reason: the warning generated here is due to a race condition
         //    while tmpnam invents the fileName it may be created by another process
         // 3. file names like "/tmp/pansen" or "C:\pansen" are platform dependent
         return std::string( std::tmpnam( NULL ) );

src/dataHandler/io/WReader.h

@@ -47,6 +47,7 @@ public:
     /**
      * Reset the file name and checks if it exists.
      *
+     * \param fname file name
      * \throws WDHNoSuchFile
      */
     void setFileName( std::string fname ) throw( WDHNoSuchFile );

src/dataHandler/io/WReaderLookUpTableVTK.h

@@ -41,11 +41,15 @@ public:
     /**
      * Creates a reader object for look up tables. On parameter documention
      * take a look into the WReader base class.
+     *
+     * \param fname file name
      */
     explicit WReaderLookUpTableVTK( std::string fname );
 
     /**
      * Perform reading from the file.
+     *
+     * \param table vector where to place the elements of the table
      */
     void readTable( boost::shared_ptr< std::vector< double > > table ) const;
 

src/dataHandler/io/WWriter.h

@@ -47,6 +47,8 @@ public:
     /**
      * Reset file name and checks if the file already exists in case of
      * non overwriting is specified.
+     *
+     * \param fname file name
      */
     void setFileName( std::string fname );
 

src/gui/CMakeLists.txt

@@ -8,6 +8,6 @@ TARGET_LINK_LIBRARIES( gui common )
 # Unit tests
 IF( CXXTEST_FOUND )
   CXXTEST_ADD_TESTS_FROM_LIST( "${GUI_SRC}"
-                               ""  # no libs for linking required
+                               "common"
                              )
 ENDIF( CXXTEST_FOUND )

src/kernel/WModule.cpp

@@ -286,3 +286,22 @@ void WModule::threadMain()
     }
 }
 
+wlog::WStreamedLogger WModule::logInfo() const
+{
+    return wlog::info( getName() );
+}
+
+wlog::WStreamedLogger WModule::logError() const
+{
+    return wlog::error( getName() );
+}
+
+wlog::WStreamedLogger WModule::logDebug() const
+{
+    return wlog::debug( getName() );
+}
+
+wlog::WStreamedLogger WModule::logWarn() const
+{
+    return wlog::warn( getName() );
+}

src/kernel/WModule.h

@@ -34,8 +34,6 @@
 #include <boost/signals2/signal.hpp>
 #include <boost/function.hpp>
 
-#include "../common/WThreadedRunner.h"
-#include "../common/WFlag.hpp"
 #include "WModuleConnectorSignals.h"
 #include "WModuleSignals.h"
 
@@ -43,7 +41,10 @@
 #include "../dataHandler/WDataSetSingle.h"
 #include "../dataHandler/WValueSet.hpp"
 
+#include "../common/WFlag.hpp"
+#include "../common/WLogger.h"
 #include "../common/WProperties.h"
+#include "../common/WThreadedRunner.h"
 
 class WModuleConnector;
 class WModuleInputConnector;
@@ -301,6 +302,14 @@ protected:
      */
     void ready();
 
+    wlog::WStreamedLogger logInfo() const;
+
+    wlog::WStreamedLogger logDebug() const;
+
+    wlog::WStreamedLogger logWarn() const;
+
+    wlog::WStreamedLogger logError() const;
+
     // **************************************************************************************************************************
     //
     // Members

src/math/WLine.h

@@ -46,15 +46,19 @@ friend class ::WLineTest;
 public:
     /**
      * Constructs a new line with the given points in the given order
+     *
+     * \param points The points this line consists of
      */
     explicit WLine( const std::vector< WPosition > &points );
 
     /**
+     * \param rhs Right hand side operand
      * \return true if both lines have a same point vector
      */
     bool operator==( const WLine &rhs ) const;
 
     /**
+     * \param rhs Right hand side operand
      * \return false if both lines have a same point vector
      */
     bool operator!=( const WLine &rhs ) const;
@@ -65,6 +69,7 @@ public:
     size_t size() const;
 
     /**
+     * \param index Index for the i'th point of this line
      * \return Const reference to the i'th position. This is const since
      * we want an read only access.
      */
@@ -73,12 +78,15 @@ public:
     /**
      * Gives a meaningful representation of this object to the given
      * output stream.
+     *
+     * \param os The outputstream
+     * \param rhs Right hand side operand
      */
     friend std::ostream& operator<<( std::ostream& os, const WLine &rhs );
 
 protected:
 private:
-    std::vector< WPosition > m_points;
+    std::vector< WPosition > m_points; //!< stores the points of this line
 };
 
 inline size_t WLine::size() const

src/math/fiberSimilarity/WZhangMetric.h

@@ -40,11 +40,17 @@ public:
     /**
      * Constructs new algorithm with its threshold for minimal square
      * distances.
+     *
+     * \param thresholdSquare Threshold upto which the distances should be
+     * ignored given as square for reasons of performance.
      */
     explicit WZhangMetric( double thresholdSquare );
 
     /**
      * Resets the threshold for minimal point distances used in computation.
+     *
+     * \param thresholdSquare Threshold upto which the distances should be
+     * ignored given as square for reasons of performance.
      */
     void setThreshold( double thresholdSquare );
 

src/modules/fiberClustering/WDXtLookUpTable.h

@@ -69,6 +69,8 @@ public:
 
     /**
      * Resets the internal data (e.g. loaded from file).
+     *
+     * \param data Vector containing the new elements
      */
     void setData( const std::vector< double > &data );
 

src/modules/fiberClustering/WMFiberClustering.cpp

@@ -26,6 +26,7 @@
 #include <iomanip>
 #include <iostream>
 #include <list>
+#include <sstream>
 #include <string>
 #include <vector>
 
@@ -106,6 +107,7 @@ void WMFiberClustering::checkDLtLookUpTable()
     {
         try
         {
+            logDebug() << "trying to read table from /tmp/pansen.dist" << std::endl;
             // TODO(math): replace this hard coded path when properties are available
             WReaderLookUpTableVTK r( "/tmp/pansen.dist" );
             using boost::shared_ptr;
@@ -132,6 +134,10 @@ void WMFiberClustering::checkDLtLookUpTable()
     {
         if( m_fibs->size() != m_lastFibsSize )
         {
+            wlog::debug( "WMFiberClustering" )
+                << "considered old table as invalid" << std::endl
+                << "current loaded fibers: " << m_fibs->size() << std::endl
+                << "old fibers: " << m_lastFibsSize << std::endl;
             // throw away old invalid table
             m_dLtTable.reset();
             m_dLtTableExists = false;
@@ -196,8 +202,9 @@ void WMFiberClustering::cluster()
                 }
             }
         }
-        std::cout << "\r" << std::fixed << std::setprecision( 2 );
-        std::cout << ( ++st ).progress() << " " << st.stringBar() << std::flush;
+        std::stringstream ss;
+        ss << "\r" << std::fixed << std::setprecision( 2 ) << ( ++st ).progress() << " " << st.stringBar() << std::flush;
+        std::cout << ss.str();
     }
     std::cout << std::endl;
     m_dLtTableExists = true;

src/utils/WColorUtils.h

@@ -35,6 +35,9 @@ namespace color_utils
 {
     /**
      * Transforms a direction given via two points into a RGB color.
+     *
+     * \param pos1 First point
+     * \param pos2 Second point
      */
      WColor getRGBAColorFromDirection( const wmath::WPosition &pos1, const wmath::WPosition &pos2 );
 }

tools/brainlint.py

@@ -192,9 +192,9 @@ _CPP_HEADERS = frozenset([
     'cstdio', 'cstdlib', 'cstring', 'ctime', 'cwchar', 'cwctype',
     'defalloc.h', 'deque.h', 'editbuf.h', 'exception', 'fstream',
     'fstream.h', 'hashtable.h', 'heap.h', 'indstream.h', 'iomanip',
-    'iomanip.h', 'ios', 'iosfwd', 'iostream', 'iostream.h', 'istream.h',
+    'iomanip.h', 'ios', 'iosfwd', 'iostream', 'iostream.h', 'istream', 'istream.h',
     'iterator.h', 'limits', 'map.h', 'multimap.h', 'multiset.h',
-    'numeric', 'ostream.h', 'parsestream.h', 'pfstream.h', 'PlotFile.h',
+    'numeric', 'ostream', 'ostream.h', 'parsestream.h', 'pfstream.h', 'PlotFile.h',
     'procbuf.h', 'pthread_alloc.h', 'rope', 'rope.h', 'ropeimpl.h',
     'SFile.h', 'slist', 'slist.h', 'stack.h', 'stdexcept',
     'stdiostream.h', 'streambuf.h', 'stream.h', 'strfile.h', 'string',