[ADD] - fiber display simple is now able to take a WDataSetFiberClustering as...

[ADD] - fiber display simple is now able to take a WDataSetFiberClustering as input and show the fibs accordingly

src/core/common/WConditionSet.h

@@ -44,6 +44,16 @@ class OWCOMMON_EXPORT WConditionSet: public WCondition
 friend class WConditionSetTest;
 public:
 
+    /**
+     * Shared pointer to instance of this class.
+     */
+    typedef boost::shared_ptr< WConditionSet > SPtr;
+
+    /**
+     * Shared pointer to const instance of this class.
+     */
+    typedef boost::shared_ptr< const WConditionSet > ConstSPtr;
+
     /**
      * Default constructor.
      */

src/core/common/exceptions/WInvalidID.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 "WInvalidID.h"
+
+WInvalidID::WInvalidID( const std::string& msg )
+    : WException( msg )
+{
+    // init members
+}
+
+WInvalidID::~WInvalidID() throw()
+{
+    // clean up
+}

src/core/common/exceptions/WInvalidID.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 WINVALIDID_H
+#define WINVALIDID_H
+
+#include <string>
+
+#include "../WException.h"
+#include "../WExportCommon.h"
+
+/**
+ * Indicates invalid element access of a container.
+ */
+class OWCOMMON_EXPORT WInvalidID : public WException
+{
+public:
+    /**
+     * Default constructor.
+     * \param msg the exception message.
+     */
+    explicit WInvalidID( const std::string& msg = "Invalid ID specified." );
+
+    /**
+     * Destructor.
+     */
+    virtual ~WInvalidID() throw();
+
+protected:
+private:
+};
+
+#endif  // WINVALIDID_H

src/core/dataHandler/WDataSetFiberClustering.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 "WDataSetFiberClustering.h"
+
+// The prototype as singleton. Created during first getPrototype() call
+boost::shared_ptr< WPrototyped > WDataSetFiberClustering::m_prototype = boost::shared_ptr< WPrototyped >();
+
+WDataSetFiberClustering::WDataSetFiberClustering()
+{
+    // initialize members
+}
+
+WDataSetFiberClustering::~WDataSetFiberClustering()
+{
+    // cleanup
+}
+
+boost::shared_ptr< WPrototyped > WDataSetFiberClustering::getPrototype()
+{
+    if( !m_prototype )
+    {
+        m_prototype = boost::shared_ptr< WPrototyped >( new WDataSetFiberClustering() );
+    }
+    return m_prototype;
+}
+
+const std::string WDataSetFiberClustering::getName() const
+{
+    return "DataSetFiberClustering";
+}
+
+const std::string WDataSetFiberClustering::getDescription() const
+{
+    return "A collection of fiber clusters.";
+}
+
+void WDataSetFiberClustering::setCluster( size_t id, WFiberCluster::SPtr cluster )
+{
+    m_clusters[ id ] = cluster;
+}
+
+WFiberCluster::SPtr WDataSetFiberClustering::getCluster( size_t id )
+{
+    WFiberCluster::SPtr result = m_clusters[ id ];
+    if( !result )
+    {
+        throw WInvalidID( "The cluster with the specified ID does not exist." );
+    }
+    return result;
+}
+
+WFiberCluster::SPtr WDataSetFiberClustering::getOrCreateCluster( size_t id )
+{
+    WFiberCluster::SPtr result = m_clusters[ id ];
+    if( !result )
+    {
+        // create an empty one
+        WFiberCluster::SPtr newCluster( new WFiberCluster() );
+        m_clusters[ id ] = newCluster;
+        return newCluster;
+    }
+    return result;
+}
+
+void WDataSetFiberClustering::removeCluster( size_t id )
+{
+    if( !m_clusters.count( id ) )
+    {
+        return;
+    }
+    m_clusters.erase( id );
+}
+
+WDataSetFiberClustering::ClusterMap::const_iterator WDataSetFiberClustering::begin() const
+{
+    return m_clusters.begin();
+}
+
+WDataSetFiberClustering::ClusterMap::iterator WDataSetFiberClustering::begin()
+{
+    return m_clusters.begin();
+}
+
+WDataSetFiberClustering::ClusterMap::const_iterator WDataSetFiberClustering::end() const
+{
+    return m_clusters.end();
+}
+
+WDataSetFiberClustering::ClusterMap::iterator WDataSetFiberClustering::end()
+{
+    return m_clusters.end();
+}
+

src/core/dataHandler/WDataSetFiberClustering.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 WDATASETFIBERCLUSTERING_H
+#define WDATASETFIBERCLUSTERING_H
+
+#include <map>
+#include <string>
+
+#include <boost/shared_ptr.hpp>
+
+#include "datastructures/WFiberCluster.h"
+
+#include "../common/exceptions/WInvalidID.h"
+#include "../common/WTransferable.h"
+
+/**
+ * This is a dataset which represent a clustering of fibers. It does not itself contain the fiber-data. This dataset only contains the indices of
+ * fibers belonging to the clusters.
+ *
+ * Each cluster has its own ID. A mapping between names and IDs is possible.
+ */
+class WDataSetFiberClustering: public WTransferable
+{
+public:
+
+    /**
+     * Convenience typedef for a boost::shared_ptr< WDataSetFiberClustering >.
+     */
+    typedef boost::shared_ptr< WDataSetFiberClustering > SPtr;
+
+    /**
+     * Convenience typedef for a boost::shared_ptr< const WDataSetFiberClustering >.
+     */
+    typedef boost::shared_ptr< const WDataSetFiberClustering > ConstSPtr;
+
+    /**
+     * The type of the cluster map
+     */
+    typedef std::map< size_t, WFiberCluster::SPtr > ClusterMap;
+
+    /**
+     * Default constructor.
+     */
+    WDataSetFiberClustering();
+
+    /**
+     * Destructor.
+     */
+    virtual ~WDataSetFiberClustering();
+
+    /**
+     * The name of this transferable. This is useful information for the users.
+     *
+     * \return the name.
+     */
+    virtual const std::string getName() const;
+
+    /**
+     *
+     * The description of this transferable. This is useful information for the users.
+     *
+     * \return A description
+     */
+    virtual const std::string getDescription() const;
+
+    /**
+     * Returns a prototype instantiated with the true type of the deriving class.
+     *
+     * \return the prototype.
+     */
+    static boost::shared_ptr< WPrototyped > getPrototype();
+
+    /**
+     * Sets the cluster at the given ID. If there is a cluster at this ID, it is replaced.
+     *
+     * \param id the ID of the cluster
+     * \param cluster the cluster
+     */
+    virtual void setCluster( size_t id, WFiberCluster::SPtr cluster );
+
+    /**
+     * Returns the cluster with the given ID.
+     *
+     * \throw WInvalidID if the ID is not known.
+     *
+     * \param id the ID of the cluster to get
+     *
+     * \return the cluster
+     */
+    virtual WFiberCluster::SPtr getCluster( size_t id );
+
+    /**
+     * Returns the cluster with the given ID. If there is no cluster with this ID, an empty one is returned.
+     *
+     * \param id the ID of the cluster to get
+     *
+     * \return the cluster
+     */
+    virtual WFiberCluster::SPtr getOrCreateCluster( size_t id );
+
+    /**
+     * Removes the cluster with the specified ID. If it does not exist, nothing happens.
+     *
+     * \param id the id of the cluster
+     */
+    virtual void removeCluster( size_t id );
+
+    /**
+     * The begin iterator of the clustering for const iteration.
+     *
+     * \return the begin iterator
+     */
+    ClusterMap::const_iterator begin() const;
+
+    /**
+     * The begin iterator of the clustering for non-const iteration.
+     *
+     * \return the begin iterator
+     */
+    ClusterMap::iterator begin();
+
+    /**
+     * The end iterator of the clustering for const iteration.
+     *
+     * \return the begin iterator
+     */
+    ClusterMap::const_iterator end() const;
+
+    /**
+     * The end iterator of the clustering for non-const iteration.
+     *
+     * \return the end iterator
+     */
+    ClusterMap::iterator end();
+
+protected:
+
+    /**
+     * Prototype for this dataset
+     */
+    static boost::shared_ptr< WPrototyped > m_prototype;
+private:
+
+    /**
+     * The map between ID and cluster.
+     */
+    std::map< size_t, WFiberCluster::SPtr > m_clusters;
+};
+
+#endif  // WDATASETFIBERCLUSTERING_H
+

src/core/dataHandler/datastructures/WFiberCluster.cpp

@@ -24,6 +24,7 @@
 
 #include <list>
 #include <vector>
+#include <algorithm>
 
 #include <boost/shared_ptr.hpp>
 
@@ -34,14 +35,8 @@
 #include "../WDataSetFiberVector.h"
 #include "WFiberCluster.h"
 
-// TODO(math): The only reason why we store here a Reference to the fiber
-// dataset is, we need it in the WMVoxelizer module as well as the clustering
-// information. Since we don't have the possibility of multiple
-// InputConnectors we must agglomerate those into one object. Please remove this.
-// initializes the variable and provides a linker reference
-// \cond Suppress_Doxygen
+// The prototype as singleton. Created during first getPrototype() call
 boost::shared_ptr< WPrototyped > WFiberCluster::m_prototype = boost::shared_ptr< WPrototyped >();
-// \endcond
 
 WFiberCluster::WFiberCluster()
     : WTransferable(),
@@ -58,6 +53,27 @@ WFiberCluster::WFiberCluster( size_t index )
     m_memberIndices.push_back( index );
 }
 
+WFiberCluster::WFiberCluster( const WFiberCluster::IndexList& indices, const WColor& color )
+    : WTransferable(),
+    m_memberIndices( indices ),
+    m_color( color ),
+    m_centerLineCreationLock( new boost::shared_mutex() ),
+    m_longestLineCreationLock( new boost::shared_mutex() )
+{
+    // init
+}
+
+WFiberCluster::WFiberCluster( WFiberCluster::IndexList::const_iterator indicesBegin,
+                              WFiberCluster::IndexList::const_iterator indicesEnd, const WColor& color )
+    : WTransferable(),
+    m_color( color ),
+    m_centerLineCreationLock( new boost::shared_mutex() ),
+    m_longestLineCreationLock( new boost::shared_mutex() )
+{
+    // now copy the index list
+    std::copy( indicesBegin, indicesEnd, m_memberIndices.begin() );
+}
+
 WFiberCluster::WFiberCluster( const WFiberCluster& other )
     : WTransferable( other ),
     m_memberIndices( other.m_memberIndices ),
@@ -88,7 +104,7 @@ WFiberCluster::~WFiberCluster()
 
 void WFiberCluster::merge( WFiberCluster& other ) // NOLINT
 {
-    std::list< size_t >::const_iterator cit = other.m_memberIndices.begin();
+    WFiberCluster::IndexList::const_iterator cit = other.m_memberIndices.begin();
     for( ; cit != other.m_memberIndices.end(); ++cit)
     {
         m_memberIndices.push_back( *cit );
@@ -99,6 +115,13 @@ void WFiberCluster::merge( WFiberCluster& other ) // NOLINT
     other.clear();
 }
 
+void WFiberCluster::merge( WFiberCluster::IndexList::const_iterator indicesBegin,
+                           WFiberCluster::IndexList::const_iterator indicesEnd )
+{
+    // now copy the index list
+    m_memberIndices.insert( m_memberIndices.end(), indicesBegin, indicesEnd );
+}
+
 // NODOXYGEN
 // \cond Suppress_Doxygen
 void WFiberCluster::setDataSetReference( boost::shared_ptr< const WDataSetFiberVector > fibs )
@@ -110,11 +133,12 @@ boost::shared_ptr< const WDataSetFiberVector > WFiberCluster::getDataSetReferenc
 {
     return m_fibs;
 }
-
 // TODO(math): The only reason why we store here a Reference to the fiber
 // dataset is, we need it in the WMVoxelizer module as well as the clustering
 // information. Since we don't have the possibility of multiple
 // InputConnectors we must agglomerate those into one object. Please remove this.
+// \endcond
+
 boost::shared_ptr< WPrototyped > WFiberCluster::getPrototype()
 {
     if( !m_prototype )
@@ -123,7 +147,6 @@ boost::shared_ptr< WPrototyped > WFiberCluster::getPrototype()
     }
     return m_prototype;
 }
-// \endcond
 
 void WFiberCluster::generateCenterLine() const
 {
@@ -139,7 +162,7 @@ void WFiberCluster::generateCenterLine() const
     // make copies of the fibers
     boost::shared_ptr< WDataSetFiberVector > fibs( new WDataSetFiberVector() );
     size_t avgFiberSize = 0;
-    for( std::list< size_t >::const_iterator cit = m_memberIndices.begin(); cit != m_memberIndices.end(); ++cit )
+    for( WFiberCluster::IndexList::const_iterator cit = m_memberIndices.begin(); cit != m_memberIndices.end(); ++cit )
     {
         fibs->push_back( m_fibs->at( *cit ) );
         avgFiberSize += fibs->back().size();
@@ -219,7 +242,7 @@ void WFiberCluster::elongateCenterLine() const
 
     // in the beginning all fibers participate
     boost::shared_ptr< WDataSetFiberVector > fibs( new WDataSetFiberVector() );
-    for( std::list< size_t >::const_iterator cit = m_memberIndices.begin(); cit != m_memberIndices.end(); ++cit )
+    for( WFiberCluster::IndexList::const_iterator cit = m_memberIndices.begin(); cit != m_memberIndices.end(); ++cit )
     {
         fibs->push_back( m_fibs->at( *cit ) );
     }
@@ -268,7 +291,7 @@ void WFiberCluster::elongateCenterLine() const
     }
     // second ending of the centerline
     boost::shared_ptr< WDataSetFiberVector > fobs( new WDataSetFiberVector() );
-    for( std::list< size_t >::const_iterator cit = m_memberIndices.begin(); cit != m_memberIndices.end(); ++cit )
+    for( WFiberCluster::IndexList::const_iterator cit = m_memberIndices.begin(); cit != m_memberIndices.end(); ++cit )
     {
         fobs->push_back( m_fibs->at( *cit ) );
     }
@@ -379,7 +402,7 @@ boost::shared_ptr< WFiber > WFiberCluster::getLongestLine() const
 WBoundingBox WFiberCluster::getBoundingBox() const
 {
     WBoundingBox result;
-    for( std::list< size_t >::const_iterator cit = m_memberIndices.begin(); cit != m_memberIndices.end(); ++cit )
+    for( WFiberCluster::IndexList::const_iterator cit = m_memberIndices.begin(); cit != m_memberIndices.end(); ++cit )
     {
         result.expandBy( computeBoundingBox( m_fibs->at( *cit ) ) );
     }

src/core/dataHandler/datastructures/WFiberCluster.h

@@ -40,10 +40,25 @@
 /**
  * Represents a cluster of indices of a WDataSetFiberVector.
  */
-class OWDATAHANDLER_EXPORT WFiberCluster : public WTransferable // NOLINT
+class OWDATAHANDLER_EXPORT WFiberCluster: public WTransferable // NOLINT
 {
 friend class WFiberClusterTest;
 public:
+    /**
+     * Shared pointer abbreviation.
+     */
+    typedef boost::shared_ptr< WFiberCluster > SPtr;
+
+    /**
+     * Const shared pointer abbreviation.
+     */
+    typedef boost::shared_ptr< const WFiberCluster > ConstSPtr;
+
+    /**
+     * This is the list of indices of fibers.
+     */
+    typedef std::list< size_t > IndexList;
+
     /**
      * Constructs an cluster with one fiber and a reference to the fiber dataset
      * to compute the intercluster distance.
@@ -52,6 +67,24 @@ public:
      */
     explicit WFiberCluster( size_t index );
 
+    /**
+     * Constructs a cluster with the specified set of indices and the given color.
+     *
+     * \param indices the indices initially used for this clustering
+     * \param color the color of this cluster
+     */
+    WFiberCluster( const IndexList& indices, const WColor& color = WColor() );
+
+    /**
+     * Constructs a clustering with the given set of indices. The indexlist is generated using the given iterators. It copies the elements in
+     * [indicesBegin,indicesEnd).
+     *
+     * \param indicesBegin begin iterator in the predefined index set
+     * \param indicesEnd end iterator in the predefined index set
+     * \param color the color of this cluster
+     */
+    WFiberCluster( IndexList::const_iterator indicesBegin, IndexList::const_iterator indicesEnd, const WColor& color = WColor() );
+
     /**
      * Copies the specified \ref WFiberCluster Instance. The copy does not contain a valid centerline or longest line.
      *
@@ -84,19 +117,28 @@ public:
      */
     void merge( WFiberCluster &other ); // NOLINT
 
+    /**
+     * Copy the elements denoted by the two iterators to this cluster. In contrast to the other merge() methods, this will not clean the source
+     * list.
+     *
+     * \param indicesBegin begin iterator in the predefined index set
+     * \param indicesEnd end iterator in the predefined index set
+     */
+    void merge( IndexList::const_iterator indicesBegin, IndexList::const_iterator indicesEnd );
+
     /**
      * Returns a const reference of all indices inside this cluster
      *
      * \return the index list
      */
-    const std::list< size_t >& getIndices() const;
+    const IndexList& getIndices() const;
 
     /**
      * Reset the indices belonging to that cluster
      *
      * \param indices list of indices
      */
-    void setIndices( const std::list< size_t >& indices );
+    void setIndices( const IndexList& indices );
 
     /**
      * Sort the indices of fibers associated with this cluster in ascending
@@ -132,18 +174,17 @@ public:
     WColor getColor() const;