[MERGE]

.hgchurn

@@ -12,3 +12,5 @@ eichelbaum@informatik.uni-leipzig.de Sebastian_Eichelbaum
 cornimueller Cornelius_Mueller
 mam04cvr@studserv.uni-leipzig.de Cornelius_Mueller
 hlawitschka@ucdavis.edu Mario_Hlawitschka
+mai02igw@informatik.uni-leipzig.de Robin_Ledig
+mai02ifw@informatik.uni-leipzig.de Robin_Ledig

src/common/datastructures/WFiberCluster.cpp

@@ -27,7 +27,7 @@
 
 #include <boost/shared_ptr.hpp>
 
-#include "../../dataHandler/WDataSetFibers.h"
+#include "../../dataHandler/WDataSetFiberVector.h"
 #include "../../math/fiberSimilarity/WDLTMetric.h"
 #include "../WLimits.h"
 #include "../WTransferable.h"
@@ -66,12 +66,12 @@ void WFiberCluster::merge( WFiberCluster& other ) // NOLINT
 
 // NODOXYGEN
 // \cond
-void WFiberCluster::setDataSetReference( boost::shared_ptr< const WDataSetFibers > fibs )
+void WFiberCluster::setDataSetReference( boost::shared_ptr< const WDataSetFiberVector > fibs )
 {
     m_fibs = fibs;
 }
 
-boost::shared_ptr< const WDataSetFibers > WFiberCluster::getDataSetReference() const
+boost::shared_ptr< const WDataSetFiberVector > WFiberCluster::getDataSetReference() const
 {
     return m_fibs;
 }

src/common/datastructures/WFiberCluster.h

@@ -31,12 +31,12 @@
 
 #include <boost/shared_ptr.hpp>
 
-#include "../../dataHandler/WDataSetFibers.h"
+#include "../../dataHandler/WDataSetFiberVector.h"
 #include "../WColor.h"
 #include "../WTransferable.h"
 
 /**
- * Represents a cluster of indices of a WDataSetFibers.
+ * Represents a cluster of indices of a WDataSetFiberVector.
  */
 class WFiberCluster : public WTransferable
 {
@@ -140,8 +140,8 @@ public:
     // InputConnectors we must agglomerate those into one object. Please remove this.
     // DISABLE DOXYGEN HERE
     // \cond
-    void setDataSetReference( boost::shared_ptr< const WDataSetFibers > fibs );
-    boost::shared_ptr< const WDataSetFibers > getDataSetReference() const;
+    void setDataSetReference( boost::shared_ptr< const WDataSetFiberVector > fibs );
+    boost::shared_ptr< const WDataSetFiberVector > getDataSetReference() const;
     static boost::shared_ptr< WPrototyped > getPrototype();
 
 protected:
@@ -163,7 +163,7 @@ private:
     /**
      * Reference to the real fibers of the brain this cluster belongs to.
      */
-    boost::shared_ptr< const WDataSetFibers > m_fibs;
+    boost::shared_ptr< const WDataSetFiberVector > m_fibs;
 
     /**
      * Color which is used to paint the members of this cluster.

src/dataHandler/WDataSetFibers2.cpp → src/dataHandler/WDataSetFiberVector.cpp

@@ -28,102 +28,77 @@
 
 #include "WDataSet.h"
 
-#include "WDataSetFibers2.h"
+#include "WDataSetFiberVector.h"
 
 // prototype instance as singleton
-boost::shared_ptr< WPrototyped > WDataSetFibers2::m_prototype = boost::shared_ptr< WPrototyped >();
+boost::shared_ptr< WPrototyped > WDataSetFiberVector::m_prototype = boost::shared_ptr< WPrototyped >();
 
-WDataSetFibers2::WDataSetFibers2()
-    : WDataSet()
+void WDataSetFiberVector::sortDescLength()
 {
-    // default constructor used by the prototype mechanism
+    std::sort( m_fibers->begin(), m_fibers->end(), wmath::hasGreaterLengthThen );
 }
 
-WDataSetFibers2::WDataSetFibers2( boost::shared_ptr< std::vector< float > >vertices,
-                boost::shared_ptr< std::vector< unsigned int > > lineStartIndexes,
-                boost::shared_ptr< std::vector< unsigned int > > lineLengths,
-                boost::shared_ptr< std::vector< unsigned int > > verticesReverse )
-    : WDataSet(),
-    m_vertices( vertices ),
-    m_lineStartIndexes( lineStartIndexes ),
-    m_lineLengths( lineLengths ),
-    m_verticesReverse( verticesReverse )
+void WDataSetFiberVector::erase( const std::vector< bool > &unused )
 {
-    for ( size_t i = 0; i < m_vertices->size(); ++i )
+    assert( unused.size() == m_fibers->size() );
+    std::vector< wmath::WFiber >::iterator useable = m_fibers->begin();
+    for( size_t i = 0 ; i < unused.size(); ++i )
     {
-        m_vertices->at( i ) = 160 - m_vertices->at( i );
-        ++i;
-        m_vertices->at( i ) = 200 - m_vertices->at( i );
-        ++i;
-        //m_pointArray[i] = m_dh->frames - m_pointArray[i];
+        if( !unused[i] )
+        {
+            *useable = ( *m_fibers )[i];
+            useable++;
+        }
     }
+    m_fibers->erase( useable, m_fibers->end() );
 }
 
-void WDataSetFibers2::sortDescLength()
-{
-    //std::sort( m_fibers->begin(), m_fibers->end(), wmath::hasGreaterLengthThen );
-}
-
-bool WDataSetFibers2::isTexture() const
+bool WDataSetFiberVector::isTexture() const
 {
     return false;
 }
 
-size_t WDataSetFibers2::size() const
+WDataSetFiberVector::WDataSetFiberVector( boost::shared_ptr< std::vector< wmath::WFiber > > fibs )
+    : WDataSet(),
+      m_fibers( fibs )
 {
-    return m_lineStartIndexes->size();
-    //return m_fibers->size();
 }
 
-//const wmath::WFiber& WDataSetFibers2::operator[]( const size_t index ) const
-//{
-//    assert( index < m_fibers->size() );
-//    return (*m_fibers)[index];
-//}
-
-const std::string WDataSetFibers2::getName() const
+WDataSetFiberVector::WDataSetFiberVector()
+    : WDataSet(),
+      m_fibers()
 {
-    return "WDataSetFibers";
+    // default constructor used by the prototype mechanism
 }
 
-const std::string WDataSetFibers2::getDescription() const
+size_t WDataSetFiberVector::size() const
 {
-    return "Contains tracked fiber data.";
+    return m_fibers->size();
 }
 
-boost::shared_ptr< WPrototyped > WDataSetFibers2::getPrototype()
+const wmath::WFiber& WDataSetFiberVector::operator[]( const size_t index ) const
 {
-    if ( !m_prototype )
-    {
-        m_prototype = boost::shared_ptr< WPrototyped >( new WDataSetFibers2() );
-    }
-
-    return m_prototype;
+    assert( index < m_fibers->size() );
+    return (*m_fibers)[index];
 }
 
-boost::shared_ptr< std::vector< float > > WDataSetFibers2::getVertices() const
+const std::string WDataSetFiberVector::getName() const
 {
-    return m_vertices;
+    return "WDataSetFiberVector";
 }
 
-boost::shared_ptr< std::vector< unsigned int > > WDataSetFibers2::getLineStartIndexes() const
+const std::string WDataSetFiberVector::getDescription() const
 {
-    return m_lineStartIndexes;
+    return "Contains tracked fiber data.";
 }
 
-boost::shared_ptr< std::vector< unsigned int > > WDataSetFibers2::getLineLengths() const
+boost::shared_ptr< WPrototyped > WDataSetFiberVector::getPrototype()
 {
-    return m_lineLengths;
-}
+    if ( !m_prototype )
+    {
+        m_prototype = boost::shared_ptr< WPrototyped >( new WDataSetFiberVector() );
+    }
 
-boost::shared_ptr< std::vector< unsigned int > > WDataSetFibers2::getVerticesReverse() const
-{
-    return m_verticesReverse;
+    return m_prototype;
 }
 
-wmath::WPosition WDataSetFibers2::getPosition( unsigned int fiber, unsigned int vertex ) const
-{
-    unsigned int index = m_lineStartIndexes->at( fiber ) * 3;
-    index += vertex * 3;
-    return wmath::WPosition( m_vertices->at( index ), m_vertices->at( index + 1 ), m_vertices->at( index + 2 ) );
-}

src/dataHandler/WDataSetFibers2.h → src/dataHandler/WDataSetFiberVector.h

@@ -22,53 +22,60 @@
 //
 //---------------------------------------------------------------------------
 
-#ifndef WDATASETFIBERS2_H
-#define WDATASETFIBERS2_H
+#ifndef WDATASETFIBERVECTOR_H
+#define WDATASETFIBERVECTOR_H
 
 #include <string>
 #include <vector>
 
 #include <boost/shared_ptr.hpp>
 
-#include "../math/WPosition.h"
-
 #include "WDataSet.h"
-
+#include "../math/WFiber.h"
 
 /**
  * Represents a simple set of WFibers.
  */
-class WDataSetFibers2 : public WDataSet
+class WDataSetFiberVector : public WDataSet
 {
 public:
     /**
-     * Constructs a new set of fibers, usage of WFiber here is for backward compatibility and should be removed
+     * Constructs a new set of WFibers
      *
-     * \param vertices
-     * \param lineStartIndexes
-     * \param lineLengths
-     * \param verticesReverse
+     * \param fibs Fiber vector to store in this data set
      */
-    WDataSetFibers2( boost::shared_ptr< std::vector< float > >vertices,
-                    boost::shared_ptr< std::vector< unsigned int > > lineStartIndexes,
-                    boost::shared_ptr< std::vector< unsigned int > > lineLengths,
-                    boost::shared_ptr< std::vector< unsigned int > > verticesReverse );
+    explicit WDataSetFiberVector( boost::shared_ptr< std::vector< wmath::WFiber > > fibs );
 
     /**
      * Constructs a new set of WFibers. The constructed instance is not usable.
      */
-    WDataSetFibers2();
+    WDataSetFiberVector();
 
     /**
      * Get number of fibers in this data set.
      */
     size_t size() const;
 
+    /**
+     * \param index The index number of the fiber which should be returned
+     * \return The i'th fiber.
+     */
+    const wmath::WFiber& operator[]( const size_t index ) const;
+
     /**
      * Sort fibers descending on their length.
      */
     void sortDescLength();
 
+    /**
+     * Deletes all those fibers which are marked true in the given
+     * unused vector.
+     *
+     * \param unused Vector having the those inidices set to true which should
+     * be deleted.
+     */
+    void erase( const std::vector< bool > &unused );
+
     /**
      * Determines whether this dataset can be used as a texture.
      *
@@ -97,34 +104,6 @@ public:
      */
     static boost::shared_ptr< WPrototyped > getPrototype();
 
-    /**
-     * Getter for m_vertices
-     */
-    boost::shared_ptr< std::vector< float > > getVertices() const;
-
-    /**
-     * Getter
-     */
-    boost::shared_ptr< std::vector< unsigned int > > getLineStartIndexes() const;
-
-    /**
-     * Getter
-     */
-    boost::shared_ptr< std::vector< unsigned int > > getLineLengths() const;
-
-    /**
-     * Getter
-     */
-    boost::shared_ptr< std::vector< unsigned int > > getVerticesReverse() const;
-
-    /**
-     * returns the position in space for a vertex of a given fiber
-     *
-     * \param fiber
-     * \param vertex
-     */
-    wmath::WPosition getPosition( unsigned int fiber, unsigned int vertex ) const;
-
 protected:
 
     /**
@@ -133,25 +112,7 @@ protected:
     static boost::shared_ptr< WPrototyped > m_prototype;
 
 private:
-    /**
-     * Point vector for all fibers that is actually usable for what we want to do
-     */
-    boost::shared_ptr< std::vector< float > > m_vertices;
-
-    /**
-     * Line vector that contains the start index for each line
-     */
-    boost::shared_ptr< std::vector< unsigned int > > m_lineStartIndexes;
-
-    /**
-     * Line vector that contains the number of vertices for each line
-     */
-    boost::shared_ptr< std::vector< unsigned int > > m_lineLengths;
-
-    /**
-     * Reverse lookup table for which point belongs to which fiber
-     */
-    boost::shared_ptr< std::vector< unsigned int > > m_verticesReverse;
+    boost::shared_ptr< std::vector< wmath::WFiber > > m_fibers; //!< stores all the fibers
 };
 
-#endif  // WDATASETFIBERS2_H
+#endif  // WDATASETFIBERVECTOR_H

src/dataHandler/WDataSetFibers.cpp

@@ -33,53 +33,45 @@
 // prototype instance as singleton
 boost::shared_ptr< WPrototyped > WDataSetFibers::m_prototype = boost::shared_ptr< WPrototyped >();
 
-void WDataSetFibers::sortDescLength()
+WDataSetFibers::WDataSetFibers()
+    : WDataSet()
 {
-    std::sort( m_fibers->begin(), m_fibers->end(), wmath::hasGreaterLengthThen );
+    // default constructor used by the prototype mechanism
 }
 
-void WDataSetFibers::erase( const std::vector< bool > &unused )
+WDataSetFibers::WDataSetFibers( boost::shared_ptr< std::vector< float > >vertices,
+                boost::shared_ptr< std::vector< size_t > > lineStartIndexes,
+                boost::shared_ptr< std::vector< size_t > > lineLengths,
+                boost::shared_ptr< std::vector< size_t > > verticesReverse )
+    : WDataSet(),
+    m_vertices( vertices ),
+    m_lineStartIndexes( lineStartIndexes ),
+    m_lineLengths( lineLengths ),
+    m_verticesReverse( verticesReverse )
 {
-    assert( unused.size() == m_fibers->size() );
-    std::vector< wmath::WFiber >::iterator useable = m_fibers->begin();
-    for( size_t i = 0 ; i < unused.size(); ++i )
+    for ( size_t i = 0; i < m_vertices->size(); ++i )
     {
-        if( !unused[i] )
-        {
-            *useable = ( *m_fibers )[i];
-            useable++;
-        }
+        m_vertices->at( i ) = 160 - m_vertices->at( i );
+        ++i;
+        m_vertices->at( i ) = 200 - m_vertices->at( i );
+        ++i;
+        //m_pointArray[i] = m_dh->frames - m_pointArray[i];
     }
-    m_fibers->erase( useable, m_fibers->end() );
-}
-
-bool WDataSetFibers::isTexture() const
-{
-    return false;
 }
 
-WDataSetFibers::WDataSetFibers( boost::shared_ptr< std::vector< wmath::WFiber > > fibs )
-    : WDataSet(),
-      m_fibers( fibs )
+void WDataSetFibers::sortDescLength()
 {
+    //std::sort( m_fibers->begin(), m_fibers->end(), wmath::hasGreaterLengthThen );
 }
 
-WDataSetFibers::WDataSetFibers()
-    : WDataSet(),
-      m_fibers()
+bool WDataSetFibers::isTexture() const
 {
-    // default constructor used by the prototype mechanism
+    return false;
 }
 
 size_t WDataSetFibers::size() const
 {
-    return m_fibers->size();
-}
-
-const wmath::WFiber& WDataSetFibers::operator[]( const size_t index ) const
-{
-    assert( index < m_fibers->size() );
-    return (*m_fibers)[index];
+    return m_lineStartIndexes->size();
 }
 
 const std::string WDataSetFibers::getName() const
@@ -102,3 +94,29 @@ boost::shared_ptr< WPrototyped > WDataSetFibers::getPrototype()
     return m_prototype;
 }
 
+boost::shared_ptr< std::vector< float > > WDataSetFibers::getVertices() const
+{
+    return m_vertices;
+}
+
+boost::shared_ptr< std::vector< size_t > > WDataSetFibers::getLineStartIndexes() const
+{
+    return m_lineStartIndexes;
+}
+
+boost::shared_ptr< std::vector< size_t > > WDataSetFibers::getLineLengths() const
+{
+    return m_lineLengths;
+}
+
+boost::shared_ptr< std::vector< size_t > > WDataSetFibers::getVerticesReverse() const
+{
+    return m_verticesReverse;
+}
+
+wmath::WPosition WDataSetFibers::getPosition( size_t fiber, size_t vertex ) const
+{
+    size_t index = m_lineStartIndexes->at( fiber ) * 3;
+    index += vertex * 3;
+    return wmath::WPosition( m_vertices->at( index ), m_vertices->at( index + 1 ), m_vertices->at( index + 2 ) );
+}

src/dataHandler/WDataSetFibers.h

@@ -30,8 +30,10 @@
 
 #include <boost/shared_ptr.hpp>
 
+#include "../math/WPosition.h"
+
 #include "WDataSet.h"
-#include "../math/WFiber.h"
+
 
 /**
  * Represents a simple set of WFibers.
@@ -40,11 +42,17 @@ class WDataSetFibers : public WDataSet
 {
 public:
     /**
-     * Constructs a new set of WFibers
+     * Constructs a new set of fibers, usage of WFiber here is for backward compatibility and should be removed
      *
-     * \param fibs Fiber vector to store in this data set
+     * \param vertices
+     * \param lineStartIndexes
+     * \param lineLengths
+     * \param verticesReverse
      */
-    explicit WDataSetFibers( boost::shared_ptr< std::vector< wmath::WFiber > > fibs );
+    WDataSetFibers( boost::shared_ptr< std::vector< float > >vertices,
+                    boost::shared_ptr< std::vector< size_t > > lineStartIndexes,
+                    boost::shared_ptr< std::vector< size_t > > lineLengths,
+                    boost::shared_ptr< std::vector< size_t > > verticesReverse );
 
     /**
      * Constructs a new set of WFibers. The constructed instance is not usable.
@@ -56,26 +64,11 @@ public:
      */
     size_t size() const;
 
-    /**
-     * \param index The index number of the fiber which should be returned
-     * \return The i'th fiber.
-     */
-    const wmath::WFiber& operator[]( const size_t index ) const;
-
     /**
      * Sort fibers descending on their length.
      */
     void sortDescLength();
 
-    /**
-     * Deletes all those fibers which are marked true in the given
-     * unused vector.
-     *
-     * \param unused Vector having the those inidices set to true which should
-     * be deleted.
-     */
-    void erase( const std::vector< bool > &unused );
-
     /**
      * Determines whether this dataset can be used as a texture.
      *
@@ -104,6 +97,34 @@ public:
      */
     static boost::shared_ptr< WPrototyped > getPrototype();
 
+    /**
+     * Getter for m_vertices
+     */
+    boost::shared_ptr< std::vector< float > > getVertices() const;
+
+    /**
+     * Getter
+     */
+    boost::shared_ptr< std::vector< size_t > > getLineStartIndexes() const;
+
+    /**
+     * Getter
+     */
+    boost::shared_ptr< std::vector< size_t > > getLineLengths() const;
+
+    /**
+     * Getter
+     */
+    boost::shared_ptr< std::vector< size_t > > getVerticesReverse() const;
+
+    /**
+     * returns the position in space for a vertex of a given fiber
+     *
+     * \param fiber
+     * \param vertex
+     */
+    wmath::WPosition getPosition( size_t fiber, size_t vertex ) const;
+
 protected:
 
     /**
@@ -112,7 +133,25 @@ protected:
     static boost::shared_ptr< WPrototyped > m_prototype;
 
 private:
-    boost::shared_ptr< std::vector< wmath::WFiber > > m_fibers; //!< stores all the fibers
+    /**
+     * Point vector for all fibers that is actually usable for what we want to do
+     */
+    boost::shared_ptr< std::vector< float > > m_vertices;
+
+    /**
+     * Line vector that contains the start index for each line
+     */
+    boost::shared_ptr< std::vector< size_t > > m_lineStartIndexes;
+
+    /**
+     * Line vector that contains the number of vertices for each line
+     */
+    boost::shared_ptr< std::vector< size_t > > m_lineLengths;
+
+    /**
+     * Reverse lookup table for which point belongs to which fiber
+     */
+    boost::shared_ptr< std::vector< size_t > > m_verticesReverse;
 };
 
 #endif  // WDATASETFIBERS_H

src/modules/marchingCubes/WTriangleMesh.h → src/dataHandler/WTriangleMesh.h

@@ -27,8 +27,8 @@
 
 #include <vector>
 
-#include "../../math/WPosition.h"
-#include "../../math/WVector3D.h"
+#include "../math/WPosition.h"
+#include "../math/WVector3D.h"
 
 /**
  * A triangle consisting of 3 id of vertices that represent its corners

src/dataHandler/exceptions/WDHParseError.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/>.
+//
+//---------------------------------------------------------------------------
+