[CHANGE] - updated module communication and infrastructure

src/OpenWalnut.cpp

@@ -64,6 +64,7 @@ int main( int argc, char* argv[] )
 
     // init the kernel
     WKernel kernel = WKernel( argc, argv, gui );
+    kernel.getRootContainer()->getModuleReadySignal()->connect( boost::bind( &WGUI::slotAddDatasetToBrowser, gui, _1 ) );
 
     return kernel.run();
 }

src/common/WProperties.h

@@ -112,6 +112,8 @@ public:
         {
             return findProp( prop )->getValue< T >();
         }
+
+        // TODO(schurade): do not use NULL as return value in this case. Throw exception instead.
         return 0;
     }
 
@@ -121,6 +123,8 @@ public:
         {
             return findProp( prop )->getMin< T >();
         }
+
+        // TODO(schurade): do not use NULL as return value in this case. Throw exception instead.
         return 0;
     }
 
@@ -130,6 +134,8 @@ public:
         {
             return findProp( prop )->getMax< T >();
         }
+
+        // TODO(schurade): do not use NULL as return value in this case. Throw exception instead.
         return 0;
     }
 

src/common/WThreadedRunner.cpp

@@ -49,12 +49,21 @@ void WThreadedRunner::wait( bool requestFinish )
 {
     if( requestFinish )
     {
-        m_FinishRequested = requestFinish;
+        // first notify
         notifyStop();
+
+        // then signal it
+        m_FinishRequested = requestFinish;
+        m_stopCondition.notify_all();
     }
     m_Thread->join();
 }
 
+void WThreadedRunner::waitForStop()
+{
+    m_stopCondition.wait( m_stopConditionMutex );
+}
+
 void WThreadedRunner::threadMain()
 {
 }

src/common/WThreadedRunner.h

@@ -25,6 +25,7 @@
 #ifndef WTHREADEDRUNNER_H
 #define WTHREADEDRUNNER_H
 
+#include <boost/thread.hpp>
 #include <boost/thread/thread.hpp>
 
 /**
@@ -91,6 +92,21 @@ protected:
      */
     void sleep( const int t ) const;
 
+    /**
+     * Let the thread sleep until a stop request was given.
+     */
+    void waitForStop();
+
+    /**
+     * Condition mutex used by m_stopCondition.
+     */
+    boost::mutex m_stopConditionMutex;
+
+    /**
+     * Condition getting fired whenever the thread should quit. This is useful for waiting for stop requests.
+     */
+    boost::condition_variable_any m_stopCondition;
+
 private:
 };
 

src/dataHandler/WDataHandler.cpp

@@ -29,7 +29,6 @@
 #include "WDataHandler.h"
 #include "WSubject.h"
 #include "exceptions/WDHNoSuchDataSet.h"
-#include "WLoaderManager.h"
 
 WDataHandler::WDataHandler()
 {
@@ -58,29 +57,3 @@ unsigned int WDataHandler::getNumberOfSubjects() const
     return m_subjects.size();
 }
 
-
-void WDataHandler::loadDataSets( std::vector< std::string > fileNames )
-{
-    WLoaderManager lm;
-    for ( size_t i = 0 ; i < fileNames.size() ; ++i)
-    {
-        try
-        {
-            lm.load( fileNames[i], shared_from_this() );
-        }
-        catch( WDHException e )
-        {
-            std::cerr << "Error :: DataHandler :: " << e.what() << std::endl;
-        }
-    }
-}
-
-void WDataHandler::signalLoadFinished( boost::shared_ptr< WDataSet > data )
-{
-    m_signalAddDataset( data );
-}
-
-boost::signal1< void, boost::shared_ptr< WDataSet > >* WDataHandler::getSignalAddDataset()
-{
-    return &m_signalAddDataset;
-}

src/dataHandler/WDataHandler.h

@@ -77,21 +77,6 @@ public:
      */
     unsigned int getNumberOfSubjects() const;
 
-    /**
-     * Calls WLoaderManager to load the given input file.
-     */
-    void loadDataSets( std::vector< std::string > fileNames );
-
-    /**
-     * is called from a loader object and signals a pointer to the loaded object
-     */
-    void signalLoadFinished( boost::shared_ptr< WDataSet > data );
-
-    /**
-     *
-     */
-    boost::signal1< void, boost::shared_ptr< WDataSet > >* getSignalAddDataset();
-
 protected:
 
 private:
@@ -99,11 +84,6 @@ private:
      * A container for all WSubjects.
      */
     std::vector< boost::shared_ptr< WSubject > > m_subjects;
-
-    /**
-    * boost signal object for signaling the addition of a dataset to the datahandler
-    */
-    boost::signal1< void, boost::shared_ptr< WDataSet > > m_signalAddDataset;
 };
 
 /**

src/dataHandler/WLoader.cpp

@@ -56,6 +56,4 @@ void WLoader::commitDataSet( boost::shared_ptr< WDataSet > data )
         subject = m_dataHandler->getSubject( 0 );
     }
     subject->addDataSet( data );
-
-    m_dataHandler->signalLoadFinished( data );
 }

src/dataHandler/WLoader.h

@@ -53,11 +53,11 @@ public:
     };
 
     /**
-     * This function is automatically called when creating a new thread for the
-     * loader with boost::thread. The method is pure virtual here to ensure
-     * that subclasses implement it.
+     * Loads the dataset.
+     * 
+     * \return the dataset loaded.
      */
-    virtual void operator()() = 0;
+    virtual boost::shared_ptr< WDataSet > load() = 0;
 
 protected:
     /**

src/dataHandler/WLoaderManager.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/thread.hpp>
-#include <boost/filesystem.hpp>
-
-#include "WLoaderManager.h"
-#include "exceptions/WDHException.h"
-#include "io/WLoaderNIfTI.h"
-#include "io/WLoaderBiosig.h"
-#include "io/WLoaderEEGASCII.h"
-#include "io/WLoaderFibers.h"
-
-std::string getSuffix( std::string name )
-{
-    boost::filesystem::path p( name );
-    return p.extension();
-}
-
-void WLoaderManager::load( std::string fileName, boost::shared_ptr< WDataHandler > dataHandler ) throw( WDHException )
-{
-    std::string suffix = getSuffix( fileName );
-
-    if( suffix == ".nii" || suffix == ".gz" )
-    {
-        if( suffix == ".gz" )  // it may be a NIfTI file too
-        {
-            boost::filesystem::path p( fileName );
-            p.replace_extension( "" );
-            suffix = getSuffix( p.string() );
-            assert( suffix == ".nii" && "currently only nii files may be gzipped" );
-        }
-        WLoaderNIfTI niiLoader( fileName, dataHandler );
-        boost::thread loaderThread( niiLoader );
-    }
-    else if( suffix == ".edf" )
-    {
-        WLoaderBiosig biosigLoader( fileName, dataHandler );
-        boost::thread loaderThread( biosigLoader );
-    }
-    else if( suffix == ".asc" )
-    {
-        WLoaderEEGASCII eegAsciiLoader( fileName, dataHandler );
-        boost::thread loaderThread( eegAsciiLoader );
-    }
-    else if( suffix == ".vtk" )
-    {
-        // This is a dummy implementation.
-        // You need to provide a real implementation here if you want to load vtk.
-        std::cout << "VTK not implemented yet" << std::endl;
-        assert( 0 );
-    }
-    else if( suffix == ".fib" )
-    {
-        WLoaderFibers fibLoader( fileName, dataHandler );
-        boost::thread loaderThread( fibLoader );
-    }
-    else
-    {
-        throw WDHException( "Unknown file type: '" + suffix + "'" );
-    }
-}
-
-
-

src/dataHandler/WLoaderManager.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 WLOADERMANAGER_H
-#define WLOADERMANAGER_H
-
-#include <string>
-
-#include <boost/shared_ptr.hpp>
-
-#include "exceptions/WDHException.h"
-
-class WDataHandler;
-
-/**
- * Decouples file loading from the rest of OpenWalnut into a single thread.
- * \ingroup dataHandler
- */
-class WLoaderManager
-{
-public:
-    /**
-     * Selects correct loader for fileName and creates loader thread.
-     */
-    void load( std::string fileName, boost::shared_ptr< WDataHandler > dataHandler ) throw( WDHException );
-protected:
-private:
-};
-
-#endif  // WLOADERMANAGER_H

src/dataHandler/io/WLoaderBiosig.cpp

@@ -56,7 +56,7 @@ void WLoaderBiosig::fillSegment( std::vector<std::vector<double> >* segment, bio
     }
 }
 
-void WLoaderBiosig::biosigLoader()
+boost::shared_ptr< WDataSet> WLoaderBiosig::load()
 {
     std::cout << "BIOSIGLOADER" << std::endl;
     hd =  sopen( m_fileName.c_str(), "r", 0 );
@@ -131,9 +131,6 @@ void WLoaderBiosig::biosigLoader()
 
     std::cout << "BIOSIG loading done." << std::endl;
     std::cout << "===================================" << std::endl;
+    return eeg;
 }
 
-void WLoaderBiosig::operator()()
-{
-    biosigLoader();
-}

src/dataHandler/io/WLoaderBiosig.h

@@ -49,13 +49,14 @@ public:
     WLoaderBiosig( std::string fileName, boost::shared_ptr< WDataHandler > dataHandler );
 
     /**
-     * This  function is automatically called when creating a new thread for the
-     * loader with boost::thread.
+     * Loads the dataset.
+     * 
+     * \return the dataset loaded.
      */
-    virtual void operator()();
+    virtual boost::shared_ptr< WDataSet > load();
+
 protected:
 private:
-    void biosigLoader();
     void fillSegment( std::vector<std::vector<double> >* segment, biosig_data_type* data );
 
     /**

src/dataHandler/io/WLoaderEEGASCII.cpp

@@ -39,7 +39,7 @@ WLoaderEEGASCII::WLoaderEEGASCII( std::string fileName, boost::shared_ptr< WData
 {
 }
 
-void WLoaderEEGASCII::operator()()
+boost::shared_ptr< WDataSet > WLoaderEEGASCII::load()
 {
     std::ifstream in( m_fileName.c_str() );
     if( in.fail() )
@@ -84,4 +84,6 @@ void WLoaderEEGASCII::operator()()
     boost::shared_ptr< WEEG > eeg = boost::shared_ptr< WEEG >( new WEEG( segments, lib, labels ) );
     eeg->setFileName( m_fileName );
     commitDataSet( eeg );
+    return eeg;
 }
+

src/dataHandler/io/WLoaderEEGASCII.h

@@ -45,10 +45,13 @@ public:
     WLoaderEEGASCII( std::string fileName, boost::shared_ptr< WDataHandler > dataHandler );
 
     /**
-     * This  function is automatically called when creating a new thread for the
-     * loader with boost::thread.
+     * Loads the dataset.
+     * 
+     * \return the dataset loaded.
      */
-    virtual void operator()();
+    virtual boost::shared_ptr< WDataSet > load();
+
+void operator()();
 
 protected:
 private:

src/dataHandler/io/WLoaderFibers.cpp

@@ -54,7 +54,7 @@ WLoaderFibers::~WLoaderFibers() throw()
 {
 }
 
-void WLoaderFibers::operator()() throw()
+boost::shared_ptr< WDataSet > WLoaderFibers::load()
 {
     using boost::shared_ptr;
     using std::vector;
@@ -81,6 +81,7 @@ void WLoaderFibers::operator()() throw()
 
     commitDataSet( fibers );
     assert( !m_ifs->is_open() );
+    return fibers;
 }
 
 void WLoaderFibers::readHeader() throw( WDHIOFailure, WDHException )

src/dataHandler/io/WLoaderFibers.h

@@ -61,10 +61,11 @@ public:
     virtual ~WLoaderFibers() throw();
 
     /**
-     * This function is automatically called when creating a new thread for the
-     * loader with boost::thread. It calls the methods of the NIfTI I/O library.
+     * Loads the dataset.
+     * 
+     * \return the dataset loaded.
      */
-    virtual void operator()() throw();
+    virtual boost::shared_ptr< WDataSet > load();
 
 protected:
     /**

src/dataHandler/io/WLoaderNIfTI.cpp

@@ -73,8 +73,7 @@ wmath::WMatrix< double > WLoaderNIfTI::convertMatrix( const mat44& in )
     return out;
 }
 
-
-void WLoaderNIfTI::operator()()
+boost::shared_ptr< WDataSet > WLoaderNIfTI::load()
 {
     nifti_image* header = nifti_image_read( m_fileName.c_str(), 0 );
     int columns = header->dim[1];
@@ -142,6 +141,8 @@ void WLoaderNIfTI::operator()()
     boost::shared_ptr< WDataSet > newDataSet = boost::shared_ptr< WDataSet >( new WDataSetSingle( newValueSet, newGrid ) );
     newDataSet->setFileName( m_fileName );
     commitDataSet( newDataSet );
+
+    return newDataSet;
 }
 
 

src/dataHandler/io/WLoaderNIfTI.h

@@ -50,10 +50,11 @@ public:
     WLoaderNIfTI( std::string fileName, boost::shared_ptr< WDataHandler > dataHandler );
 
     /**
-     * This function is automatically called when creating a new thread for the
-     * loader with boost::thread. It calls the methods of the NIfTI I/O library.
+     * Loads the dataset.
+     * 
+     * \return the dataset loaded.
      */
-    virtual void operator()();
+    virtual boost::shared_ptr< WDataSet > load();
 
 protected:
 private:

src/dataHandler/io/test/WLoaderEEGASCII_test.h

@@ -51,7 +51,7 @@ public:
         TS_ASSERT_EQUALS( dataHandler->getNumberOfSubjects(), 0 );
 
         WLoaderEEGASCII eegASCIILoader( fileName, dataHandler );
-        boost::thread loaderThread( eegASCIILoader );
+        eegASCIILoader.load();
 
         std::clock_t startTime;
         startTime = std::clock();

src/dataHandler/io/test/WLoaderFibers_test.h

@@ -276,7 +276,7 @@ public:
     {
         TS_ASSERT_EQUALS( m_dataHandler->getNumberOfSubjects(), 0 );
         WLoaderFibers loader( "fixtures/Fibers/valid_small_example.fib", m_dataHandler );
-        loader();
+        loader.load();
         TS_ASSERT_EQUALS( m_dataHandler->getNumberOfSubjects(), 1 );
     }
 

src/dataHandler/test/WLoaderManager_test.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 WLOADERMANAGER_TEST_H
-#define WLOADERMANAGER_TEST_H
-
-#include <ctime>
-#include <string>
-#include <iostream>
-
-#include <boost/shared_ptr.hpp>
-#include <boost/timer.hpp>
-#include <cxxtest/TestSuite.h>
-
-
-#include "../WDataHandler.h"
-#include "../WLoaderManager.h"
-#include "../WDataSet.h"
-
-/**
- * Testsuite for WLoaderManager.
- */
-class WLoaderManagerTest : public CxxTest::TestSuite
-{
-public:
-    /**
-     * The load routine should manage to select the appropriate WLoader class
-     * for a file type.
-     */
-    void testLoad( void )
-    {
-        std::string fileName = "fixtures/scalar_signed_short.nii.gz";
-        std::cout << std::endl << "Test loading of " << fileName << "." << std::endl;
-        boost::shared_ptr< WDataHandler > dataHandler = boost::shared_ptr< WDataHandler >( new WDataHandler() );
-        TS_ASSERT_EQUALS( dataHandler->getNumberOfSubjects(), 0 );
-        WLoaderManager testLoaderManager;
-        testLoaderManager.load( fileName, dataHandler );
-
-        std::clock_t startTime;
-        startTime = std::clock();
-        std::clock_t elapsedTime = 0;
-
-        while( dataHandler->getNumberOfSubjects() == 0  && ( elapsedTime / static_cast< double >( CLOCKS_PER_SEC ) ) < 4 )
-        {
-            elapsedTime = std::clock() - startTime;
-        }
-
-        // TODO(wiebel): we need to change this because loading, in the end,
-        // should not always increase the number of subjects.
-        TS_ASSERT_EQUALS( dataHandler->getNumberOfSubjects(), 1 );
-    }
-};
-
-#endif  // WLOADERMANAGER_TEST_H

src/dataHandler/test/WLoader_test.h

@@ -30,6 +30,7 @@
 #include <cxxtest/TestSuite.h>
 
 #include "../WLoader.h"
+#include "../WDataSet.h"
 
 /**
  * Just a dummy for testing the base class
@@ -42,7 +43,7 @@ public:
     {
     }
 
-    virtual void operator()()
+    virtual boost::shared_ptr< WDataSet > load()
     {
     }
 };

src/gui/WGUI.cpp

@@ -27,3 +27,9 @@
 WGUI::~WGUI()
 {
 }
+
+void WGUI::slotAddDatasetToBrowser( boost::shared_ptr< WModule > module )
+{
+    addDatasetToBrowser( module, 0 );
+}
+

src/gui/WGUI.h

@@ -52,6 +52,13 @@ public:
      */
     virtual void createMainWindow() = 0;
 
+    /**
+     * Slot gets called whenever a new module is added.
+     * 
+     * \param module
+     */
+    virtual void slotAddDatasetToBrowser( boost::shared_ptr< WModule > module );
+
     /**
      *  adds a dataset to the dataset browser for a give subject
      */

src/kernel/WKernel.cpp

@@ -35,12 +35,6 @@
 
 #include "WModule.h"
 #include "WModuleFactory.h"
-#include "../modules/data/WMData.hpp"
-#include "../modules/navSlices/WMNavSlices.h"
-#include "../modules/coordinateSystem/WMCoordinateSystem.h"
-#include "../modules/fiberDisplay/WMFiberDisplay.h"
-#include "../modules/fiberCulling/WMFiberCulling.h"
-#include "../modules/fiberClustering/WMFiberClustering.h"
 #include "../common/WException.h"
 
 #include "../graphicsEngine/WGraphicsEngine.h"
@@ -66,8 +60,7 @@ WKernel::WKernel( int argc, char* argv[], boost::shared_ptr< WGUI > gui )
 
     // get module factory
     m_moduleFactory = WModuleFactory::getModuleFactory();
-    m_moduleContainer = boost::shared_ptr< WModuleContainer >( new WModuleContainer( "KernelRootContainer",
-                "Root module container in Kernel." ) );
+    m_moduleContainer = boost::shared_ptr< WModuleContainer >();
 
     // init GE, DataHandler, ...
     init();
@@ -145,56 +138,19 @@ int WKernel::run()
 
     // run? data handler stuff?
 
-    // **************************************************************************************************************************
-    // This part will be exchanged by some kind of ModuleContainer managing module execution.
-    // TODO(ebaum): replace by ModuleContainer
-    // **************************************************************************************************************************
-
-    // run module execution threads
-    // TODO(ebaum): after having modules loaded they should be started here.
-    // currently this is just the test module
-    /*
-    WLogger::getLogger()->addLogMessage( "*** Starting modules:", "Kernel", LL_DEBUG );
-    for( std::list< boost::shared_ptr< WModule > >::iterator list_iter = m_modules.begin(); list_iter != m_modules.end();