[MERGE]

.hgignore

@@ -23,3 +23,7 @@ syntax: glob
 .cproject
 syntax: regexp
 ^Debug$
+syntax: glob
+.settings
+syntax: glob
+Release

doc/developer/designDocuments/Makefile

+all:
+	pdflatex openWalnutDesign
+	pdflatex openWalnutDesign
+	bibtex openWalnutDesign
+	bibtex openWalnutDesign
+	pdflatex openWalnutDesign
+	pdflatex openWalnutDesign
+	cp openWalnutDesign.pdf openWalnutDesignDocument.pdf
+clean:
+	rm openWalnutDesign.aux openWalnutDesign.log openWalnutDesign.out openWalnutDesign.toc openWalnutDesign.bbl openWalnutDesign.blg openWalnutDesign.pdf openWalnutDesignDocument.pdf

doc/developer/designDocuments/openWalnutDesign.tex

@@ -66,6 +66,8 @@ section stem from the following website:
   \includegraphics[width=\textwidth]{WValue_hierachy}
   \caption{The class hierarchy describing high-level values in OpenWalnut.}
 \end{figure}
+\section{Literature}
+For a general overview on visualization in medicine \cite{Preim:2007:VMT} can be recommended.
 
 \chapter{GUI}
 The GUI module is the only part where we allow gui-toolkit related code. For example, this means that the use of any QT class is
@@ -122,6 +124,6 @@ myValuePointer = getValuesPointer<float *>()
 \begin{itemize}
 \item Data can not be manipulated!
 \end{itemize}
- 
 
+\bibliography{../../books}
 \end{document}

src/CMakeLists.txt

@@ -15,6 +15,8 @@ IF( CMAKE_HOST_SYSTEM MATCHES Linux )
   SET( LIBRARY_OUTPUT_PATH ${PROJECT_BINARY_DIR}/lib CACHE PATH "The libraries will be put into this directory." )
 ELSEIF( CMAKE_HOST_SYSTEM MATCHES Windows )
   SET( LIBRARY_OUTPUT_PATH ${PROJECT_BINARY_DIR}/bin CACHE PATH "The libraries will be put into this directory." )
+ELSEIF( CMAKE_HOST_SYSTEM MATCHES Darwin )
+  SET( LIBRARY_OUTPUT_PATH ${PROJECT_BINARY_DIR}/lib CACHE PATH "The libraries will be put into this directory." )
 ELSE()
   MESSAGE( FATAL_ERROR "Could not determine platform type! (expected Linux or Windows)!" )
 ENDIF()
@@ -30,7 +32,7 @@ ENDIF( CMAKE_BUILD_TYPE STREQUAL "Static" )
 # To see which boost libs we currently use, you may run the following command
 # in the trunk/src directory on a linux box to make some investigations:
 # grep -i include `find . -type f` | grep boost | awk '{print $2}' | sort | uniq
-FIND_PACKAGE( Boost REQUIRED program_options thread filesystem signals )
+FIND_PACKAGE( Boost REQUIRED program_options thread system filesystem date_time signals )
 ASSERT_GE_VERSION( "Boost" "${Boost_MAJOR_VERSION}.${Boost_MINOR_VERSION}.${Boost_SUBMINOR_VERSION}" 1.36.0 )
 INCLUDE_DIRECTORIES( ${Boost_INCLUDE_DIR} )
 
@@ -54,10 +56,11 @@ FIND_PACKAGE( osg ${MIN_OSG_VERSION} REQUIRED )
 FIND_PACKAGE( osgUtil ${MIN_OSG_VERSION} REQUIRED )
 FIND_PACKAGE( osgDB ${MIN_OSG_VERSION} REQUIRED )
 FIND_PACKAGE( osgViewer ${MIN_OSG_VERSION} REQUIRED )
+FIND_PACKAGE( osgText ${MIN_OSG_VERSION} REQUIRED )
 FIND_PACKAGE( osgGA ${MIN_OSG_VERSION} REQUIRED )
 FIND_PACKAGE( OpenThreads ${MIN_OSG_VERSION} REQUIRED )
-SET( OPENSCENEGRAPH_LIBRARIES ${OSGDB_LIBRARY} ${OSGGA_LIBRARY} ${OSGUTIL_LIBRARY} ${OSGVIEWER_LIBRARY} ${OSG_LIBRARY} ${OPENTHREADS_LIBRARY} )
-SET( OPENSCENEGRAPH_INCLUDE_DIRS ${OSG_INCLUDE_DIR} ${OSGDB_INCLUDE_DIR} ${OSGGA_INCLUDE_DIR} ${OSGVIEWER_INCLUDE_DIR} ${OSGUTIL_INCLUDE_DIR} ${OPENTHREADS_INCLUDE_DIR} )
+SET( OPENSCENEGRAPH_LIBRARIES ${OSGDB_LIBRARY} ${OSGTEXT_LIBRARY} ${OSGGA_LIBRARY} ${OSGUTIL_LIBRARY} ${OSGVIEWER_LIBRARY} ${OSG_LIBRARY} ${OPENTHREADS_LIBRARY} )
+SET( OPENSCENEGRAPH_INCLUDE_DIRS ${OSG_INCLUDE_DIR} ${OSGDB_INCLUDE_DIR} ${OSGTEXT_INCLUDE_DIR} ${OSGGA_INCLUDE_DIR} ${OSGVIEWER_INCLUDE_DIR} ${OSGUTIL_INCLUDE_DIR} ${OPENTHREADS_INCLUDE_DIR} )
 # When new cmake version available >=2.6.4 we may use this the line below instead the stuff above
 # FIND_PACKAGE( OpenSceneGraph 2.8.0 REQUIRED osgDB osgUtil osgGA osgViewer OpenThreads )
 INCLUDE_DIRECTORIES( ${OPENSCENEGRAPH_INCLUDE_DIRS} )
@@ -95,7 +98,7 @@ IF( NOT CMAKE_BUILD_TYPE STREQUAL "Static" )
     ADD_SUBDIRECTORY( kernel )
     ADD_SUBDIRECTORY( common )
     ADD_EXECUTABLE( walnut OpenWalnut.cpp utils/WOptionHandler.cpp )
-    TARGET_LINK_LIBRARIES( walnut kernel dataHandler guiqt4 common ${Boost_LIBRARIES} )
+    TARGET_LINK_LIBRARIES( walnut kernel dataHandler gui guiqt4 common ${Boost_LIBRARIES} )
     
 ELSE( NOT CMAKE_BUILD_TYPE STREQUAL "Static" )
     FILE( GLOB_RECURSE ALL_SRC ${PROJECT_SOURCE_DIR}/*.cpp )
@@ -104,7 +107,6 @@ ELSE( NOT CMAKE_BUILD_TYPE STREQUAL "Static" )
 
     # Package dependencies:
     FIND_PACKAGE( Qt4 REQUIRED )
-    FIND_PACKAGE( GLEW REQUIRED )
 
     # Includes:
     INCLUDE_DIRECTORIES( ${QT_INCLUDE_DIR} )
@@ -118,7 +120,7 @@ ELSE( NOT CMAKE_BUILD_TYPE STREQUAL "Static" )
     QT4_WRAP_CPP( GUI_QT4_MOC_SRCS ${GUI_QT4_MOC_HDRS} )
     
     ADD_EXECUTABLE( walnut ${ALL_SRC}  ${NIFTI_SRC} ${GUI_QT4_MOC_SRCS} )
-    TARGET_LINK_LIBRARIES( walnut ${Boost_LIBRARIES} ${OSG_LIBRARIES} ${QT_LINK_LIBRARIES} ${GLEW_LIBRARY} )
+    TARGET_LINK_LIBRARIES( walnut ${Boost_LIBRARIES} ${OSG_LIBRARIES} ${QT_LINK_LIBRARIES} )
 ENDIF ( NOT CMAKE_BUILD_TYPE STREQUAL "Static" )
 
 execute_process(COMMAND ${CMAKE_COMMAND} -E make_directory ${CMAKE_BINARY_DIR}/bin/shaders)
@@ -207,7 +209,7 @@ ADD_CUSTOM_TARGET( cleantest
 #-------------------------------------------------------------------------------------------------------------
 # Checks if all is well to commit (aka commitCheck, cicheck)
 ADD_CUSTOM_TARGET( cicheck
-                   COMMAND make test && make stylecheck
+                   COMMAND make stylecheck && make test
                    COMMENT "Checks if all is well to commit"
                  )
 
@@ -227,3 +229,12 @@ ADD_CUSTOM_TARGET( many
                    cmake . && make all -j4 && make fixtures && make stylecheck && make test && make doc
                    COMMENT "Make many special make targets in combination."
                  )
+
+#-------------------------------------------------------------------------------------------------------------
+# Make target for MacOS. The difference to the normal one is that we need to fix some paths in libraries.
+IF( CMAKE_HOST_SYSTEM MATCHES Darwin )
+ADD_CUSTOM_TARGET( macos
+                   make all && ${PROJECT_SOURCE_DIR}/../tools/MacOS/macOS_install_tool 
+                   COMMENT "Make on MacOS. This incudes fixing paths in libraries."
+                 )
+ENDIF()

src/OpenWalnut.cpp

@@ -26,6 +26,10 @@
 
 #include "common/WException.h"
 #include "common/WSegmentationFault.h"
+#include "common/WLogger.h"
+
+#include "gui/WGUI.h"
+#include "gui/qt4/WMainApplication.h"
 
 #include "kernel/WKernel.h"
 
@@ -51,8 +55,16 @@ int main( int argc, char* argv[] )
     // install signal handler as early as possible
     WSegmentationFault::installSignalHandler();
 
+    // initialize GUI
+    boost::shared_ptr< WGUI > gui = boost::shared_ptr< WGUI >( new WMainApplication() );
+
+    // init logger
+    WLogger logger;
+    logger.run();
+
     // init the kernel
-    WKernel kernel = WKernel( argc, argv );
+    WKernel kernel = WKernel( argc, argv, gui );
+
     int code = kernel.run();
     return code;
 }

src/common/WLogEntry.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 <string>
+
+#include <boost/algorithm/string.hpp>
+
+#include "WLogEntry.h"
+
+WLogEntry:: WLogEntry( std::string logTime, std::string message, LogLevel level, std::string source )
+    : m_time( logTime ),
+      m_message( message ),
+      m_level( level ),
+      m_source( source )
+{
+}
+
+WLogEntry::~WLogEntry()
+{
+}
+
+std::string WLogEntry::getLogString( std::string format )
+{
+    std::string s = format;
+
+    boost::ireplace_first( s, "%t", m_time );
+
+    switch ( m_level )
+    {
+        case LL_DEBUG:
+            boost::ireplace_first( s, "%l", "DEBUG  " );
+            break;
+        case LL_INFO:
+            boost::ireplace_first( s, "%l", "INFO   " );
+            break;
+        case LL_WARNING:
+            boost::ireplace_first( s, "%l", "WARNING" );
+            break;
+        case LL_ERROR:
+            boost::ireplace_first( s, "%l", "ERROR  " );
+            break;
+        default:
+            break;
+    }
+
+    boost::ireplace_first( s, "%m", m_message );
+
+    boost::ireplace_first( s, "%s", m_source );
+
+    return s;
+}
+
+LogLevel WLogEntry::getLogLevel()
+{
+    return m_level;
+}

src/common/WLogEntry.h

+//---------------------------------------------------------------------------
+//
+// 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/>.
+//
+//---------------------------------------------------------------------------
+
+#ifndef WLOGENTRY_H
+#define WLOGENTRY_H
+
+#include <string>
+
+/**
+ * Various log levels, to distinguish output on its level.
+ */
+typedef enum
+{
+    LL_DEBUG = 0,
+    LL_INFO,
+    LL_WARNING,
+    LL_ERROR
+}
+LogLevel;
+
+/**
+ * Represents a simple log message with some attributes.
+ */
+class WLogEntry
+{
+public:
+    /**
+     * Construtcs a log message entry
+     */
+    WLogEntry( std::string logTime, std::string message, LogLevel level, std::string source = "" );
+
+    /**
+     * Destroys a log message entry.
+     */
+    virtual ~WLogEntry();
+
+    /**
+     * \return String of this log entry.
+     */
+    std::string getLogString( std::string format = "[%t] *%l* %m \n" );
+
+    /**
+     * \return log level of this entry.
+     */
+    LogLevel getLogLevel();
+
+protected:
+private:
+    /**
+     * The time the log message was received
+     */
+    std::string m_time;
+
+    /**
+     * The actual message
+     */
+    std::string m_message;
+
+    /**
+     * Log level
+     */
+    LogLevel m_level;
+
+    /**
+     * Source (e.g. module name) where this log message comes from.
+     */
+    std::string m_source;
+};
+
+#endif  // WLOGENTRY_H

src/common/WLogger.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 <iostream>
+#include <string>
+
+#include <boost/date_time/posix_time/posix_time.hpp>
+#include <boost/filesystem/fstream.hpp>
+
+#include "WLogger.h"
+
+/**
+ * Used for program wide access to the logger.
+ */
+WLogger* logger = NULL;
+
+WLogger::WLogger( std::string fileName, LogLevel level ):
+    WThreadedRunner(),
+    m_LogLevel( level ),
+
+    m_STDOUTLevel( level ),
+    m_STDERRLevel( LL_ERROR ),
+    m_LogFileLevel( level ),
+    m_LogFileName( fileName ),
+    m_QueueMutex()
+{
+    logger = this;
+
+    addLogMessage( "Initalizing Logger", "Logger", LL_DEBUG );
+    addLogMessage( "===============================================================================", "Logger", LL_INFO );
+    addLogMessage( "=                          Starting Log Session                               =", "Logger", LL_INFO );
+    addLogMessage( "===============================================================================", "Logger", LL_INFO );
+}
+
+WLogger::~WLogger()
+{
+}
+
+WLogger* WLogger::getLogger()
+{
+    return logger;
+}
+
+void WLogger::setLogLevel( LogLevel level )
+{
+    m_LogLevel = level;
+}
+
+void WLogger::setSTDOUTLevel( LogLevel level )
+{
+    m_STDOUTLevel = level;
+}
+
+void WLogger::setSTDERRLevel( LogLevel level )
+{
+    m_STDERRLevel = level;
+}
+
+void WLogger::setLogFileLevel( LogLevel level )
+{
+    m_LogFileLevel = level;
+}
+
+void WLogger::setLogFileName( std::string fileName )
+{
+    boost::filesystem::path p( fileName );
+
+    // TODO(schurade): check if this is a _VALID_ path (existence is not needed)
+
+    m_LogFileName = fileName;
+}
+
+void WLogger::addLogMessage( std::string message, std::string source, LogLevel level )
+{
+    if ( m_LogLevel > level || m_FinishRequested )
+    {
+        return;
+    }
+
+    boost::posix_time::ptime t( boost::posix_time::second_clock::local_time() );
+    std::string timeString( to_simple_string( t ) );
+    WLogEntry entry( timeString, message, level, source );
+
+    boost::mutex::scoped_lock l( m_QueueMutex );
+    m_LogQueue.push( entry );
+}
+
+void WLogger::processQueue()
+{
+    boost::mutex::scoped_lock l( m_QueueMutex );
+
+    while ( !m_LogQueue.empty() )
+    {
+        WLogEntry entry = m_LogQueue.front();
+        m_LogQueue.pop();
+
+        m_SessionLog.push_back( entry );
+
+        if ( entry.getLogLevel() >= m_STDOUTLevel )
+        {
+            std::cout << entry.getLogString();
+        }
+
+        if ( entry.getLogLevel() >= m_STDERRLevel )
+        {
+            std::cerr << entry.getLogString();
+        }
+
+        if ( entry.getLogLevel() >= m_LogFileLevel )
+        {
+            // TODO(schurade): first open file, then write to file, then close the file
+            // for atomic file usage.
+            boost::filesystem::path p( "walnut.log" );
+            boost::filesystem::ofstream ofs( p, boost::filesystem::ofstream::app );
+            ofs << entry.getLogString();
+        }
+    }
+}
+
+void WLogger::threadMain()
+{
+    // Since the modules run in a separate thread: such loops are possible
+    while ( !m_FinishRequested )
+    {
+        processQueue();
+        // do fancy stuff
+        sleep( 1 );
+    }
+
+    // clean up stuff
+}

src/dataHandler/io/test/WLoaderVTK_test.h → src/common/WLogger.h

@@ -22,104 +22,134 @@
 //
 //---------------------------------------------------------------------------
 
-#ifndef WLOADERVTK_TEST_H
-#define WLOADERVTK_TEST_H
+#ifndef WLOGGER_H
+#define WLOGGER_H
 
+#include <queue>
 #include <string>
 #include <vector>
 
-#include <boost/filesystem.hpp>
-#include <cxxtest/TestSuite.h>
+#include <boost/shared_ptr.hpp>
+#include <boost/thread/thread.hpp>
+#include <boost/thread/mutex.hpp>
+#include <boost/thread/locks.hpp>
+#include "../common/WThreadedRunner.h"
 
-#include "../WLoaderVTK.h"
-#include "../../WDataHandler.h"
+#include "WLogEntry.h"
 
 /**
- * Unit tests the WLoaderVTK class.
+ * Does actual logging of WLogEntries down to stdout or something similar.
  */
-class WLoaderVTKTest : public CxxTest::TestSuite
+class WLogger: public WThreadedRunner
 {
 public:
     /**
-     * Create test environment.
-     */
-    void setUp( void )
-    {
-        m_dataHandler = boost::shared_ptr< WDataHandler >( new WDataHandler() );
-        m_vtkFile = boost::filesystem::path( "fixtures/VTK/ascii-2nd-order-tensor.vtk" );
-        assert( boost::filesystem::exists( m_vtkFile ) );
-    }
-
-    /**
-     * A valid "header" of a VTK file consists of 4 lines of text (this is
-     * arbitrary specified by me, the author of this class)
-     * 1. VTK version stuff
-     * 2. VTK description header stuff (max 256 chars)
-     * 3. BINARY or ASCII
-     * 4. DATASET type
-     * 
-     * Further description about the DATASET e.g. ORIGIN in case of
-     * STRUCTURED_POINTS does not belong to the header.
+     * Constructor
+     */
+    WLogger( std::string fileName = "walnut.log", LogLevel level = LL_DEBUG );
+
+    /**
+     * Destructor.
+     */
+    virtual ~WLogger();
+
+    /**
+     * Returns pointer to the currently running logger instance.
      *
-     * FYI: It makes really sense to restrict the header to 4 lines since since
-     * every VTK file must have at least 4 lines describing in ASCII what comes
-     * next.
-     */
-    void testReadHeader( void )
-    {
-        WLoaderVTK loader( m_vtkFile.string(), m_dataHandler );
-        loader.readHeader();
-        std::vector< std::string > expected;
-        expected.push_back( "# vtk DataFile Version 3.0" );
-        expected.push_back( "vtk output" );
-        expected.push_back( "ASCII" );
-        expected.push_back( "DATASET STRUCTURED_POINTS" );
-        TS_ASSERT_EQUALS( loader.m_header, expected );
-    }
-
-    /**
-     * If the path is not valid there should be thrown an exception
-     */
-    void testReadHeaderOnInvalidFile( void )
-    {
-        WLoaderVTK loader( "no/such/file", m_dataHandler );
-        TS_ASSERT_THROWS_EQUALS( loader.readHeader(),
-                                 const WDHIOFailure &e,
-                                 e.what(),
-                                 std::string( "Invalid file or filename: no/such/file" ) );
-    }
-
-    /**
-     * If the header introduces a STRUCTURED_POINTS VTK DATASET then true
-     * should be returned.
-     */
-    void testCheckDatasetType( void )
-    {
-        WLoaderVTK loader( m_vtkFile.string(), m_dataHandler );
-        loader.readHeader();
-        TS_ASSERT_EQUALS( loader.datasetTypeIs( "STRUCTURED_POINTS" ), true );
-    }
-
-    /**
-     * A VTK file is typically either in BINARY or ASCII format.
-     */
-    void testBinaryOrAscii( void )
-    {
-        WLoaderVTK loader( m_vtkFile.string(), m_dataHandler );
-        loader.readHeader();
-        TS_ASSERT_EQUALS( loader.isBinary(), false );
-    }
+     * \return pointer to logger instance.
+     */
+    static WLogger* getLogger();
+
+    /**
+     * Sets the global log level
+     */
+    void setLogLevel( LogLevel level );
+
+    /**
+     * Sets the log level for stdout.
+     */
+    void setSTDOUTLevel( LogLevel level );
+
+    /**
+     * Sets the log level for stderr.
+     */
+    void setSTDERRLevel( LogLevel level );
+
+    /**
+     * Sets the log level for the given log file.
+     */
+    void setLogFileLevel( LogLevel level );
+
+    /**
+     * Specifies the path for logging to this file and checks if the path
+     * exists by an assertion.
+     */
+    void setLogFileName( std::string fileName );
+
+    /**
+     * Appends a log message to the logging queue.
+     */
+    void addLogMessage( std::string message, std::string source = "", LogLevel level = LL_DEBUG );
+
+    /**
+     * Locks this logging instance for threadsafeness and prints the
+     * items of the queue.
+     */
+    void processQueue();
+
+    /**
+     * Entry point after loading the module. Runs in separate thread.
+     */
+    virtual void threadMain();
+
+protected:
 
 private: