[CHANGE] - adopted voxelizer to new dataset types

- added property for parameterization algorithm selection
- modules now use std::vector for connector management -> adding-order used for compatibility test

src/dataHandler/datastructures/WFiberCluster.cpp

@@ -42,16 +42,39 @@ boost::shared_ptr< WPrototyped > WFiberCluster::m_prototype = boost::shared_ptr<
 // \endcond
 
 WFiberCluster::WFiberCluster()
-    : WTransferable()
+    : WTransferable(),
+    m_centerLineCreationLock( new boost::shared_mutex() ),
+    m_longestLineCreationLock( new boost::shared_mutex() )
 {
 }
 
 WFiberCluster::WFiberCluster( size_t index )
-    : WTransferable()
+    : WTransferable(),
+    m_centerLineCreationLock( new boost::shared_mutex() ),
+    m_longestLineCreationLock( new boost::shared_mutex() )
 {
     m_memberIndices.push_back( index );
 }
 
+WFiberCluster::WFiberCluster( const WFiberCluster& other )
+    : WTransferable( other ),
+    m_memberIndices( other.m_memberIndices ),
+    m_fibs( other.m_fibs ),
+    m_color( other.m_color ),
+    m_centerLineCreationLock( new boost::shared_mutex() ),  // do not copy the mutex as both instances of WFiberCluster can be modifed at the
+                                                            // same time
+    m_longestLineCreationLock( new boost::shared_mutex() ),
+    m_centerLine(  boost::shared_ptr< wmath::WFiber >( new wmath::WFiber( *other.m_centerLine.get() ) ) ),
+    m_longestLine(  boost::shared_ptr< wmath::WFiber >( new wmath::WFiber( *other.m_longestLine.get() ) ) )
+{
+}
+
+WFiberCluster::~WFiberCluster()
+{
+    delete m_centerLineCreationLock;
+    delete m_longestLineCreationLock;
+}
+
 void WFiberCluster::merge( WFiberCluster& other ) // NOLINT
 {
     std::list< size_t >::const_iterator cit = other.m_memberIndices.begin();
@@ -89,8 +112,17 @@ boost::shared_ptr< WPrototyped > WFiberCluster::getPrototype()
 }
 // \endcond
 
-void WFiberCluster::generateCenterLine()
+void WFiberCluster::generateCenterLine() const
 {
+    // ensure nobody changes the mutable m_centerline
+    boost::unique_lock< boost::shared_mutex > lock = boost::unique_lock< boost::shared_mutex >( *m_centerLineCreationLock );
+    // has the line been calculated while we waited?
+    if ( m_centerLine )
+    {
+        lock.unlock();
+        return;
+    }
+
     // make copies of the fibers
     boost::shared_ptr< WDataSetFiberVector > fibs( new WDataSetFiberVector() );
     size_t avgFiberSize = 0;
@@ -120,6 +152,46 @@ void WFiberCluster::generateCenterLine()
         avgPosition /= fibs->size();
         m_centerLine->push_back( avgPosition );
     }
+
+    lock.unlock();
+}
+
+void WFiberCluster::generateLongestLine() const
+{
+    // ensure nobody changes the mutable m_longestline
+    boost::unique_lock< boost::shared_mutex > lock = boost::unique_lock< boost::shared_mutex >( *m_longestLineCreationLock );
+    // has the line been calculated while we waited?
+    if ( m_longestLine )
+    {
+        lock.unlock();
+        return;
+    }
+
+    m_longestLine = boost::shared_ptr< wmath::WFiber >( new wmath::WFiber() );
+
+    // empty datasets can be ignored
+    if ( m_fibs->size() == 0 )
+    {
+        return;
+    }
+
+    size_t longest = 0;
+    size_t longestID = 0;
+    for( size_t cit = 0; cit < m_fibs->size(); ++cit )
+    {
+        if ( m_fibs->at( cit ).size() > longest )
+        {
+            longest = m_fibs->at( cit ).size();
+            longestID = cit;
+        }
+    }
+
+    for ( wmath::WFiber::const_iterator cit = m_fibs->at( longestID ).begin(); cit != m_fibs->at( longestID ).end(); ++cit )
+    {
+        m_longestLine->push_back( *cit );
+    }
+
+    lock.unlock();
 }
 
 void WFiberCluster::unifyDirection( boost::shared_ptr< WDataSetFiberVector > fibs ) const
@@ -160,5 +232,19 @@ void WFiberCluster::unifyDirection( boost::shared_ptr< WDataSetFiberVector > fib
 
 boost::shared_ptr< wmath::WFiber > WFiberCluster::getCenterLine() const
 {
+    if ( !m_centerLine )
+    {
+        generateCenterLine();
+    }
     return m_centerLine;
 }
+
+boost::shared_ptr< wmath::WFiber > WFiberCluster::getLongestLine() const
+{
+    if ( !m_longestLine )
+    {
+        generateLongestLine();
+    }
+    return m_longestLine;
+}
+

src/dataHandler/datastructures/WFiberCluster.h

@@ -30,6 +30,7 @@
 #include <vector>
 
 #include <boost/shared_ptr.hpp>
+#include <boost/thread.hpp>
 
 #include "../../common/WColor.h"
 #include "../../common/WTransferable.h"
@@ -50,11 +51,23 @@ public:
      */
     explicit WFiberCluster( size_t index );
 
+    /**
+     * Copies the specified \ref WFiberCluster Instance. The copy does not contain a valid centerline or longest line.
+     *
+     * \param other the other instance to clone.
+     */
+    WFiberCluster( const WFiberCluster& other );
+
     /**
      * Constructs an empty cluster.
      */
     WFiberCluster();
 
+    /**
+     * Destructs. Frees used locks/mutex.
+     */
+    virtual ~WFiberCluster();
+
     /**
      * Returns true if there are no fibers in that cluster, false otherwise.
      */
@@ -152,16 +165,28 @@ public:
     // \endcond
 
     /**
-     * Returns the center line of this cluster
+     * Returns the center line of this cluster. The centerline gets calculated during the first call of this method.
      *
      * \return Reference to the center line
      */
     boost::shared_ptr< wmath::WFiber > getCenterLine() const;
 
+    /**
+     * Returns the center line of this cluster. The longest line gets calculated during the first call if this method.
+     *
+     * \return Reference to the longest line
+     */
+    boost::shared_ptr< wmath::WFiber > getLongestLine() const;
+
     /**
      * Makes the hard work to compute the center line.
      */
-    void generateCenterLine();
+    void generateCenterLine() const;
+
+    /**
+     * Makes the hard work to find the longest line.
+     */
+    void generateLongestLine() const;
 
 protected:
     // TODO(math): The only reason why we store here a Reference to the fiber
@@ -200,7 +225,29 @@ private:
      */
     WColor m_color;
 
-    boost::shared_ptr< wmath::WFiber > m_centerLine; //!< Average fiber for this cluster representing the main direction and curvatur of this cluster
+    /**
+     * Lock the modification in the m_centerLine mutable. The lock is stored as pointer to avoid copy construction problems.
+     */
+    boost::shared_mutex* m_centerLineCreationLock;
+
+    /**
+     * Lock the modification in the m_longestLine mutable. The lock is stored as pointer to avoid copy construction problems.
+     */
+    boost::shared_mutex* m_longestLineCreationLock;
+
+    /**
+     * Average fiber for this cluster representing the main direction and curvature of this cluster.
+     *
+     * \note This member is mutable as it needs to be modified during a const getter.
+     */
+    mutable boost::shared_ptr< wmath::WFiber > m_centerLine;
+
+    /**
+     * The longest fiber in the dataset.
+     *
+     * \note This member is mutable as it needs to be modified during a const getter.
+     */
+    mutable boost::shared_ptr< wmath::WFiber > m_longestLine;
 };
 
 inline bool WFiberCluster::empty() const

src/gui/qt4/datasetbrowser/WQtTreeItem.cpp

@@ -93,18 +93,18 @@ void WQtTreeItem::updateTooltip( std::string progress )
 
     // also list the connectors
     std::string conList = "";
-    std::set< boost::shared_ptr< WModuleInputConnector > > cons = m_module->getInputConnectors();
-    std::set< boost::shared_ptr< WModuleOutputConnector > > consOut = m_module->getOutputConnectors();
+    WModule::InputConnectorList cons = m_module->getInputConnectors();
+    WModule::OutputConnectorList consOut = m_module->getOutputConnectors();
     conList += "<table><tr><th>Name</th><th>Description</th><th>Connected</th></tr>";
     int conCount = 0;
-    for ( std::set< boost::shared_ptr< WModuleInputConnector > >::const_iterator it = cons.begin(); it != cons.end(); ++it )
+    for ( WModule::InputConnectorList::const_iterator it = cons.begin(); it != cons.end(); ++it )
     {
         ++conCount;
         conList += "<tr><td><b>" + ( *it )->getName() + "&nbsp;</b></td><td>&nbsp;" + ( *it )->getDescription() + "&nbsp;</td>";
         conList += ( *it )->isConnected() ? "<td>&nbsp;yes&nbsp;</td>" : "<td>&nbsp;no&nbsp;</td>";
         conList += "</tr>";
     }
-    for ( std::set< boost::shared_ptr< WModuleOutputConnector > >::const_iterator it = consOut.begin(); it != consOut.end(); ++it )
+    for ( WModule::OutputConnectorList::const_iterator it = consOut.begin(); it != consOut.end(); ++it )
     {
         ++conCount;
         conList += "<tr><td><b>" + ( *it )->getName() + "&nbsp;</b></td><td>&nbsp;" + ( *it )->getDescription() + "&nbsp;</td>";

src/kernel/WModule.cpp

@@ -26,6 +26,7 @@
 #include <sys/prctl.h>
 #endif
 
+#include <algorithm>
 #include <set>
 #include <string>
 #include <sstream>
@@ -95,23 +96,29 @@ WModule::~WModule()
 
 void WModule::addConnector( boost::shared_ptr< WModuleInputConnector > con )
 {
-    m_inputConnectors.insert( con );
+    if ( std::count( m_inputConnectors.begin(), m_inputConnectors.end(), con ) == 0 )
+    {
+        m_inputConnectors.push_back( con );
+    }
 }
 
 void WModule::addConnector( boost::shared_ptr< WModuleOutputConnector > con )
 {
-    m_outputConnectors.insert( con );
+    if ( std::count( m_outputConnectors.begin(), m_outputConnectors.end(), con ) == 0 )
+    {
+        m_outputConnectors.push_back( con );
+    }
 }
 
 void WModule::disconnect()
 {
     // remove connections and their signals
-    for( std::set<boost::shared_ptr< WModuleInputConnector > >::iterator listIter = m_inputConnectors.begin();
+    for( InputConnectorList::iterator listIter = m_inputConnectors.begin();
          listIter != m_inputConnectors.end(); ++listIter )
     {
         ( *listIter )->disconnectAll();
     }
-    for( std::set<boost::shared_ptr< WModuleOutputConnector > >::iterator listIter = m_outputConnectors.begin();
+    for( OutputConnectorList::iterator listIter = m_outputConnectors.begin();
          listIter != m_outputConnectors.end(); ++listIter )
     {
         ( *listIter )->disconnectAll();
@@ -184,12 +191,12 @@ MODULE_TYPE WModule::getType() const
     return MODULE_ARBITRARY;
 }
 
-const std::set<boost::shared_ptr< WModuleInputConnector > >& WModule::getInputConnectors() const
+const WModule::InputConnectorList& WModule::getInputConnectors() const
 {
     return m_inputConnectors;
 }
 
-const std::set<boost::shared_ptr< WModuleOutputConnector > >& WModule::getOutputConnectors() const
+const WModule::OutputConnectorList& WModule::getOutputConnectors() const
 {
     return m_outputConnectors;
 }
@@ -197,7 +204,7 @@ const std::set<boost::shared_ptr< WModuleOutputConnector > >& WModule::getOutput
 boost::shared_ptr< WModuleInputConnector > WModule::getInputConnector( std::string name )
 {
     // simply search
-    for( std::set<boost::shared_ptr< WModuleInputConnector > >::const_iterator listIter = m_inputConnectors.begin();
+    for( InputConnectorList::const_iterator listIter = m_inputConnectors.begin();
          listIter != m_inputConnectors.end(); ++listIter )
     {
         // try the canonical name
@@ -213,7 +220,7 @@ boost::shared_ptr< WModuleInputConnector > WModule::getInputConnector( std::stri
 boost::shared_ptr< WModuleOutputConnector > WModule::getOutputConnector( std::string name )
 {
     // simply search
-    for( std::set<boost::shared_ptr< WModuleOutputConnector > >::const_iterator listIter = m_outputConnectors.begin();
+    for( OutputConnectorList::const_iterator listIter = m_outputConnectors.begin();
          listIter != m_outputConnectors.end(); ++listIter )
     {
         // try the canonical name

src/kernel/WModule.h

@@ -82,12 +82,22 @@ public:
      */
     virtual ~WModule();
 
+    /**
+     * The type for the list of input connectors.
+     */
+    typedef std::vector< boost::shared_ptr< WModuleInputConnector > > InputConnectorList;
+
+    /**
+     * The type for the list of output connectors.
+     */
+    typedef std::vector< boost::shared_ptr< WModuleOutputConnector > > OutputConnectorList;
+
     /**
      * Gives back input connectors.
      *
      * \return the input connectors.
      */
-    const std::set< boost::shared_ptr< WModuleInputConnector > >& getInputConnectors() const;
+    const InputConnectorList& getInputConnectors() const;
 
     /**
      * Finds the named connector for the module.
@@ -104,7 +114,7 @@ public:
      *
      * \return the output connectors.
      */
-    const std::set< boost::shared_ptr< WModuleOutputConnector > >& getOutputConnectors() const;
+    const OutputConnectorList& getOutputConnectors() const;
 
     /**
      * Finds the named connector for the module.
@@ -470,14 +480,13 @@ protected:
 
     /**
      * Set of input connectors associated with this module.
-     * NOTE: we need a thread safe list implementation!
      */
-    std::set<boost::shared_ptr< WModuleInputConnector > > m_inputConnectors;
+    InputConnectorList m_inputConnectors;
 
     /**
      * Set of output connectors associated with this module.
      */
-    std::set<boost::shared_ptr< WModuleOutputConnector > > m_outputConnectors;
+    OutputConnectorList m_outputConnectors;
 
     /**
      * True whenever the module should be active

src/kernel/WModuleContainer.cpp

@@ -367,9 +367,9 @@ boost::shared_ptr< WModule > WModuleContainer::applyModule( boost::shared_ptr< W
     // crashed module has set some data on its output and some other module needs it. -> so we ignore the case of crashed modules here.
 
     // get offered outputs
-    std::set<boost::shared_ptr<WModuleInputConnector> > ins = m->getInputConnectors();
+    WModule::InputConnectorList ins = m->getInputConnectors();
     // get offered inputs
-    std::set<boost::shared_ptr<WModuleOutputConnector> > outs = applyOn->getOutputConnectors();
+    WModule::OutputConnectorList outs = applyOn->getOutputConnectors();
 
     // TODO(ebaum): search best matching instead of simply connecting both
     if ( !ins.empty() && !outs.empty() )

src/kernel/WModuleFactory.cpp

@@ -259,7 +259,7 @@ std::vector< boost::shared_ptr< WApplyPrototypeCombiner > > WModuleFactory::getC
             ++listIter )
     {
         // get connectors of this prototype
-        std::set<boost::shared_ptr<WModuleInputConnector> > pcons = ( *listIter )->getInputConnectors();
+        WModule::InputConnectorList pcons = ( *listIter )->getInputConnectors();
         if(  pcons.size() == 0  )
         {
             // NOTE: it is OK here to use the variable module even if it is NULL as the combiner in this case only adds the specified module
@@ -274,7 +274,7 @@ std::vector< boost::shared_ptr< WApplyPrototypeCombiner > > WModuleFactory::getC
     }
 
     // get offered outputs
-    std::set<boost::shared_ptr<WModuleOutputConnector> > cons = module->getOutputConnectors();
+    WModule::OutputConnectorList cons = module->getOutputConnectors();
 
     // return early if we have no output connector, because the modules with no input connector
     // are already added at this point.
@@ -296,7 +296,7 @@ std::vector< boost::shared_ptr< WApplyPrototypeCombiner > > WModuleFactory::getC
             ++listIter )
     {
         // get connectors of this prototype
-        std::set<boost::shared_ptr<WModuleInputConnector> > pcons = ( *listIter )->getInputConnectors();
+        WModule::InputConnectorList pcons = ( *listIter )->getInputConnectors();
 
         // ensure we have 1 connector
         if( pcons.size() == 0 )

src/kernel/combiner/WModuleProjectFileCombiner.cpp

@@ -403,8 +403,8 @@ void WModuleProjectFileCombiner::save( std::ostream& output )   // NOLINT
     for ( WModuleContainer::ModuleConstIterator iter = container->get().begin(); iter != container->get().end(); ++iter )
     {
         // iterate over all outputs
-        const std::set< boost::shared_ptr< WModuleOutputConnector > >& outs = ( *iter )->getOutputConnectors();
-        for ( std::set< boost::shared_ptr< WModuleOutputConnector > >::const_iterator citer = outs.begin(); citer != outs.end(); ++citer )
+        const WModule::OutputConnectorList& outs = ( *iter )->getOutputConnectors();
+        for ( WModule::OutputConnectorList::const_iterator citer = outs.begin(); citer != outs.end(); ++citer )
         {
             // iterate over all connections:
             // TODO(ebaum): iterating over a protected member variable? Thats ugly. This should be adopted to WSharedAccess

src/modules/voxelizer/WCenterlineParameterization.cpp

@@ -44,10 +44,10 @@ WCenterlineParameterization::~WCenterlineParameterization()
     // cleanup
 }
 
-boost::shared_ptr< WDataSetSingle > WCenterlineParameterization::getDataSet()
+boost::shared_ptr< WDataSetScalar > WCenterlineParameterization::getDataSet()
 {
     boost::shared_ptr< WValueSet< double > > valueSet( new WValueSet< double >( 0, 1, m_paramFinalValues, W_DT_DOUBLE ) );
-    return boost::shared_ptr< WDataSetSingle >( new WDataSetSingle( valueSet, m_grid ) );
+    return boost::shared_ptr< WDataSetScalar >( new WDataSetScalar( valueSet, m_grid ) );
 }
 
 namespace

src/modules/voxelizer/WCenterlineParameterization.h

@@ -70,7 +70,7 @@ public:
      *
      * \return the dataset.
      */
-    virtual boost::shared_ptr< WDataSetSingle > getDataSet();
+    virtual boost::shared_ptr< WDataSetScalar > getDataSet();
 
     /**
      * Gets called for each new line getting rasterized. Here, it is used to reset the internal length integrator

src/modules/voxelizer/WDirectionParameterization.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 "WDirectionParameterization.h"
-
-WDirectionParameterization::WDirectionParameterization( boost::shared_ptr< WGridRegular3D > grid ):
-    WRasterParameterization( grid ),
-    m_dirValues( 3 * grid->size(), 0.0 )
-{
-    // initialize members
-}
-
-WDirectionParameterization::~WDirectionParameterization()
-{
-    // cleanup
-}
-
-boost::shared_ptr< WDataSetSingle > WDirectionParameterization::getDataSet()
-{
-    boost::shared_ptr< WValueSet< double > > valueSet( new WValueSet< double >( 1, 3, m_dirValues, W_DT_DOUBLE ) );
-    return boost::shared_ptr< WDataSetSingle >( new WDataSetSingle( valueSet, m_grid ) );
-}
-
-void WDirectionParameterization::parameterizeVoxel( const wmath::WValue< int >& /*voxel*/, size_t voxelId, const int /*axis*/,
-                                                    const double /*value*/,
-                                                    const wmath::WPosition& start,
-                                                    const wmath::WPosition& end )
-{
-    // segment end and start point define its direction
-    wmath::WPosition vec = end - start;
-
-    m_dirValues[ ( 3 * voxelId )     ] = vec[0];
-    m_dirValues[ ( 3 * voxelId ) + 1 ] = vec[1];
-    m_dirValues[ ( 3 * voxelId ) + 2 ] = vec[2];
-}
-

src/modules/voxelizer/WDirectionParameterization.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 WDIRECTIONPARAMETERIZATION_H
-#define WDIRECTIONPARAMETERIZATION_H
-
-#include <vector>
-
-#include "WRasterParameterization.h"
-
-/**
- * Stores the direction if a line in a separate dataset for each voxel.
- */
-class WDirectionParameterization: public WRasterParameterization
-{
-public:
-
-    /**
-     * Default constructor.
-     *
-     * \param grid the grid used for the new dataset.
-     */
-    explicit WDirectionParameterization( boost::shared_ptr< WGridRegular3D > grid );
-
-    /**
-     * Destructor.
-     */
-    virtual ~WDirectionParameterization();
-
-    /**
-     * This method allows this parameterization to update. It gets called for every voxel which is rasterized by the WRasterAlgorithm.
-     *
-     * \param voxel the voxel to parameterize
-     * \param voxelIdx the voxel index in the common grid calculated using "voxel" (this is for convenience)
-     * \param axis  Along which axis the traversal takes place. Since when walking in e.g. X-direction there are not supporting voxels in the
-     * \param value the new voxel value
-     * \param start Start point of the line segement (used to computed the distance)
-     * \param end   End point of the line segement (used to computed the distance)
-     */
-    virtual void parameterizeVoxel( const wmath::WValue< int >& voxel, size_t voxelIdx, const int axis, const double value,
-                                    const wmath::WPosition& start,
-                                    const wmath::WPosition& end );
-
-    /**
-     * Gets the dataset representing the parameterization.
-     *
-     * \return the dataset.
-     */
-    virtual boost::shared_ptr< WDataSetSingle > getDataSet();
-
-protected:
-
-    /**
-     * Stores the direction of the fiber at each voxel.
-     */
-    std::vector< double > m_dirValues;
-
-private:
-};
-
-#endif  // WDIRECTIONPARAMETERIZATION_H
-

src/modules/voxelizer/WIntegrationParameterization.cpp

@@ -37,10 +37,10 @@ WIntegrationParameterization::~WIntegrationParameterization()
     // cleanup
 }
 
-boost::shared_ptr< WDataSetSingle > WIntegrationParameterization::getDataSet()
+boost::shared_ptr< WDataSetScalar > WIntegrationParameterization::getDataSet()
 {
     boost::shared_ptr< WValueSet< double > > valueSet( new WValueSet< double >( 0, 1, m_lengthValues, W_DT_DOUBLE ) );
-    return boost::shared_ptr< WDataSetSingle >( new WDataSetSingle( valueSet, m_grid ) );
+    return boost::shared_ptr< WDataSetScalar >( new WDataSetScalar( valueSet, m_grid ) );
 }