[MERGE]

.hg_notify.hgml

 [usersubs]
-allopenwalnutcommits@dergrosse.de = *
-math@informatik.uni-leipzig.de = *
-ebaum@informatik.uni-leipzig.de = *
-reichenbach@informatik.uni-leipzig.de = *
-philips@zimbra.cbs.mpg.de = *
-wiebel@informatik.uni-leipzig.de = *
\ No newline at end of file
+all-openwalnut-commits@lists.informatik.uni-leipzig.de = *
\ No newline at end of file

doc/user/walnut.cfg.devel

@@ -55,6 +55,14 @@ compatiblesToolBarPos = 0 # position of the compatibles toolbar (overrides toolB
 # dsbInvisibleByDefault = yes # hide the control panel on startup. Can be shown using F9.
 # dsbFloatingByDefault = yes  # should the control panel be undocked on startup?
 
+# Here you can put any key sequence you would like to result in removing modules or ROIs
+# Examples: 
+# deleteKey = Backspace
+# deleteKey = Ctrl+J
+# deleteKey = B
+deleteModuleKey = Backspace
+deleteROIKey = Del
+
 ####################################################################
 # Other GUI settings
 

doc/user/walnut.cfg.mpi

@@ -9,7 +9,7 @@
 # default=HUD
 ## A list of modules that will be provided through the GUI. 
 ## If the list is empty all available modules are provided.
-whiteList = Arbitrary Plane,Coordinate System,Image Extractor,Paint Texture,Arbitrary Rois,Bounding Box,Distance Map Isosurface,Gauss Filtering,HUD,Isosurface,Isosurface Raytracer,LIC,Read Mesh,Voxelizer,Superquadric Glyphs,Triangle Mesh Renderer,Vector Plot,Write NIfTI
+whiteList = Arbitrary Plane,Coordinate System,Image Extractor,Paint Texture,Arbitrary Rois,Bounding Box,Distance Map Isosurface,Gauss Filtering,HUD,Isosurface,Isosurface Raytracer,LIC,Read Mesh,Voxelizer,Superquadric Glyphs,Triangle Mesh Renderer,Vector Plot,Write NIfTI,Fiber Display
 
 ## Specify a ";" separated list of additional paths for modules. The order of appearance is the order of loading. The following additional rules apply here:
 ## 1. if the directory contains one or more libOWmodule_XYZ it/they get loaded
@@ -58,6 +58,14 @@ compatiblesToolBarPos = 0 # position of the compatibles toolbar (overrides toolB
 # dsbInvisibleByDefault = yes # hide the control panel on startup. Can be shown using F9.
 # dsbFloatingByDefault = yes  # should the control panel be undocked on startup?
 
+# Here you can put any key sequence you would like to result in removing modules or ROIs
+# Examples: 
+# deleteKey = Backspace
+# deleteKey = Ctrl+J
+# deleteKey = B
+deleteModuleKey = Backspace
+deleteROIKey = Del
+
 ####################################################################
 # Other GUI settings
 

src/common/WHierarchicalTree.cpp

@@ -36,24 +36,288 @@ WHierarchicalTree::~WHierarchicalTree()
 {
 }
 
-void WHierarchicalTree::addCluster( size_t cluster1, size_t cluster2, float customData )
+std::vector< size_t > WHierarchicalTree::findXBiggestClusters( size_t cluster, size_t number )
 {
-    m_leafesLocked = true;
+    //std::cout << number << " largest clusters for cluster: " << cluster << std::endl;
 
-    size_t level = std::max( m_level[cluster1], m_level[cluster1] ) + 1;
-    m_level.push_back( level );
+    if ( number > m_containsLeafes[cluster].size() )
+    {
+        number = m_containsLeafes[cluster].size();
+    }
 
-    m_maxLevel = std::max( m_maxLevel, level );
+    // init
+    std::list<size_t>worklist;
+    worklist.push_back( cluster );
 
-    m_parents.push_back( m_clusterCount );
-    m_customData.push_back( customData );
-    m_colors.push_back( WColor( 0.3, 0.3, 0.3, 1.0 ) );
+    while ( worklist.size() < number )
+    {
+        size_t current = worklist.front();
+        worklist.pop_front();
+        if ( m_containsLeafes[current].size() > 1 )
+        {
+            size_t left = m_children[current].first;
+            size_t right = m_children[current].second;
+            worklist.push_back( left );
+            worklist.push_back( right );
+        }
+        else
+        {
+            worklist.push_back( current );
+        }
+    }
+    sortList( worklist );
 
-    std::pair<size_t, size_t>childs( cluster1, cluster2 );
-    m_children.push_back( childs );
+    bool newSplit = true;
 
-    m_parents[cluster1] = m_clusterCount;
-    m_parents[cluster2] = m_clusterCount;
+    while ( newSplit )
+    {
+        newSplit = false;
+        size_t current = worklist.front();
 
-    ++m_clusterCount;
+        if ( m_containsLeafes[current].size() > 1 )
+        {
+            size_t left = m_children[current].first;
+            size_t right = m_children[current].second;
+            size_t last = worklist.back();
+
+            if ( m_containsLeafes[left].size() > m_containsLeafes[last].size() )
+            {
+                worklist.pop_front();
+                worklist.push_back( left );
+                sortList( worklist );
+                newSplit = true;
+            }
+
+            last = worklist.back();
+            if ( m_containsLeafes[right].size() > m_containsLeafes[last].size() )
+            {
+                if ( !newSplit )
+                {
+                    worklist.pop_front();
+                }
+                if ( worklist.size() == number )
+                {
+                    worklist.pop_back();
+                }
+                worklist.push_back( right );
+                sortList( worklist );
+                newSplit = true;
+            }
+        }
+        sortList( worklist );
+    }
+
+    std::vector<size_t>returnVector;
+    std::list<size_t>::iterator it;
+    for ( it = worklist.begin(); it != worklist.end(); ++it )
+    {
+        size_t current = *it;
+        //std::cout << "cluster:" << current << "  size:" << m_containsLeafes[current].size() << std::endl;
+        returnVector.push_back( current );
+    }
+
+    return returnVector;
+}
+
+std::vector< size_t > WHierarchicalTree::findXBiggestClusters2( size_t cluster, size_t number )
+{
+    //std::cout << number << " largest clusters for cluster: " << cluster << std::endl;
+
+    if ( number > m_containsLeafes[cluster].size() )
+    {
+        number = m_containsLeafes[cluster].size();
+    }
+
+    // init
+    std::list<size_t>worklist;
+    worklist.push_back( cluster );
+
+    while ( worklist.size() < number )
+    {
+        size_t current = worklist.front();
+        worklist.pop_front();
+        if ( m_containsLeafes[current].size() > 1 )
+        {
+            size_t left = m_children[current].first;
+            size_t right = m_children[current].second;
+            worklist.push_back( left );
+            worklist.push_back( right );
+        }
+        else
+        {
+            worklist.push_back( current );
+        }
+    }
+    sortList( worklist );
+
+    bool newSplit = true;
+
+    while ( newSplit )
+    {
+        newSplit = false;
+        size_t current = worklist.front();
+
+        if ( m_containsLeafes[current].size() > 1 )
+        {
+            size_t left = m_children[current].first;
+            size_t right = m_children[current].second;
+            size_t last = worklist.back();
+
+            if ( ( m_containsLeafes[left].size() > m_containsLeafes[last].size() ) &&
+                 ( m_containsLeafes[right].size() > m_containsLeafes[last].size() ) )
+            {
+                if ( m_containsLeafes[left].size() > m_containsLeafes[last].size() )
+                {
+                    worklist.pop_front();
+                    worklist.push_back( left );
+                    sortList( worklist );
+                    newSplit = true;
+                }
+
+                last = worklist.back();
+                if ( m_containsLeafes[right].size() > m_containsLeafes[last].size() )
+                {
+                    if ( !newSplit )
+                    {
+                        worklist.pop_front();
+                    }
+                    if ( worklist.size() == number )
+                    {
+                        worklist.pop_back();
+                    }
+                    worklist.push_back( right );
+                    sortList( worklist );
+                    newSplit = true;
+                }
+            }
+        }
+        sortList( worklist );
+    }
+
+    std::vector<size_t>returnVector;
+    std::list<size_t>::iterator it;
+    for ( it = worklist.begin(); it != worklist.end(); ++it )
+    {
+        size_t current = *it;
+        //std::cout << "cluster:" << current << "  size:" << m_containsLeafes[current].size() << std::endl;
+        returnVector.push_back( current );
+    }
+
+    return returnVector;
+}
+
+
+std::vector< size_t > WHierarchicalTree::downXLevelsFromTop( size_t level, bool hideOutliers )
+{
+    if ( level > m_maxLevel )
+    {
+        level = m_maxLevel -1;
+    }
+
+    std::vector<size_t>returnVector;
+
+    std::list<size_t>worklist;
+    worklist.push_back( m_clusterCount - 1 );
+
+    for ( size_t i = 0; i < level; ++i )
+    {
+        std::list<size_t>newChildList;
+        while ( !worklist.empty() )
+        {
+            size_t current = worklist.front();
+            worklist.pop_front();
+            if ( m_containsLeafes[current].size() > 1 )
+            {
+                size_t left = m_children[current].first;
+                size_t right = m_children[current].second;
+
+                if ( hideOutliers )
+                {
+                    if ( m_containsLeafes[left].size() > 1 )
+                    {
+                        newChildList.push_back( left );
+                    }
+                    if ( m_containsLeafes[right].size() > 1 )
+                    {
+                        newChildList.push_back( right );
+                    }
+                }
+                else
+                {
+                    newChildList.push_back( left );
+                    newChildList.push_back( right );
+                }
+            }
+        }
+        worklist = newChildList;
+    }
+
+    sortList( worklist );
+
+    std::list<size_t>::iterator it;
+    for ( it = worklist.begin(); it != worklist.end(); ++it )
+    {
+        size_t current = *it;
+        returnVector.push_back( current );
+    }
+
+    return returnVector;
+}
+
+
+void WHierarchicalTree::sortList( std::list<size_t> &input ) //NOLINT
+{
+    if ( input.size() == 0 )
+    {
+        return;
+    }
+
+    std::vector<size_t>vec;
+    std::list<size_t>::iterator it;
+
+    for ( it = input.begin(); it != input.end(); ++it )
+    {
+        vec.push_back( *it );
+    }
+
+    for ( size_t n = vec.size() - 1; n > 0; --n )
+    {
+        for ( size_t i = 0; i < n; ++i )
+        {
+            if ( m_containsLeafes[vec[i]].size() < m_containsLeafes[vec[i+1]].size() )
+            {
+                size_t tmp = vec[i];
+                vec[i] = vec[i+1];
+                vec[i+1] = tmp;
+            }
+        }
+    }
+
+    input.clear();
+    for ( size_t k = 0; k < vec.size(); ++k )
+    {
+        input.push_back( vec[k] );
+    }
+}
+
+void WHierarchicalTree::colorCluster( size_t cluster, WColor color )
+{
+    std::list<size_t>worklist;
+    worklist.push_back( cluster );
+
+    while ( !worklist.empty() )
+    {
+        size_t current = worklist.front();
+        worklist.pop_front();
+
+        m_colors[current] = color;
+
+        if ( m_containsLeafes[current].size() > 1 )
+        {
+            size_t left = m_children[current].first;
+            size_t right = m_children[current].second;
+            worklist.push_back( left );
+            worklist.push_back( right );
+        }
+    }
 }

src/common/WHierarchicalTree.h

@@ -58,15 +58,6 @@ public:
      */
     virtual void addLeaf() = 0;
 
-    /**
-     * adds a cluster to the set, it combines 2 already existing clusters
-     *
-     * \param cluster1 first cluster to add
-     * \param cluster2 second cluster to add
-     * \param customData some arbitrary data stored with the cluster
-     */
-    void addCluster( size_t cluster1, size_t cluster2, float customData );
-
     /**
      * getter
      * \return the number of leafes
@@ -127,19 +118,12 @@ public:
      */
     std::pair<size_t, size_t>getChildren( size_t cluster );
 
-    /**
-     * sets the color for a selected cluster and all sub clusters
-     * \param cluster
-     * \param color
-     */
-    virtual void colorCluster( size_t cluster, WColor color ) = 0;
-
     /**
      * getter
      * \param cluster
      * \return the leafes contained in the selected cluster
      */
-    virtual std::vector<size_t>getLeafesForCluster( size_t cluster ) = 0;
+    std::vector<size_t>getLeafesForCluster( size_t cluster );
 
     /**
      * getter
@@ -155,6 +139,45 @@ public:
      */
     bool isLeaf( size_t cluster );
 
+    /**
+     * returns a number of clusters at a certain level down from top cluster
+     * \param level how many levels to go down
+     * \param hideOutliers true if clusters of size 1 should be ignored
+     * \return vector containing the cluster id's
+     */
+    std::vector< size_t >downXLevelsFromTop( size_t level, bool hideOutliers = false );
+
+    /**
+     * finds the X biggest clusters for a given cluster
+     * \param cluster
+     * \param number of sub clusters
+     */
+    std::vector< size_t >findXBiggestClusters( size_t cluster, size_t number = 10 );
+
+    // TODO(schurade): merge these two function
+    /**
+     * finds the X biggest clusters for a given cluster
+     * \param cluster
+     * \param number of sub clusters
+     */
+    std::vector< size_t >findXBiggestClusters2( size_t cluster, size_t number = 10 );
+
+
+    /**
+     * helper function to sort a list of clusters depending on the number of leafes in them
+     * \param input reference to the list to be sorted
+     */
+    void sortList( std::list<size_t> &input ); //NOLINT
+
+
+    /**
+     * sets the color for a selected cluster and all sub clusters
+     * \param cluster
+     * \param color
+     */
+    void colorCluster( size_t cluster, WColor color );
+
+
 protected:
     /**
      * overall number of cluster, counts both leafes ( clusters of size one ) and real clusters
@@ -202,6 +225,13 @@ protected:
      * a color value for each cluster
      */
     std::vector<WColor>m_colors;
+
+    /**
+     *vector that stores the leaf id's for each cluster, this is quite memory intensive but speeds up selection
+     * of leafes for nodes at higher levels
+     */
+    std::vector< std::vector<size_t> >m_containsLeafes;
+
 private:
 };
 
@@ -276,4 +306,9 @@ inline bool WHierarchicalTree::isLeaf( size_t cluster )
     return ( cluster < m_leafCount ) ? true : false;
 }
 
+inline std::vector<size_t>WHierarchicalTree::getLeafesForCluster( size_t cluster )
+{
+    return m_containsLeafes[cluster];
+}
+
 #endif  // WHIERARCHICALTREE_H

src/common/WHierarchicalTreeFibers.cpp

@@ -29,8 +29,6 @@
 #include <queue>
 #include <list>
 
-#include "../kernel/WKernel.h"
-
 #include "WHierarchicalTreeFibers.h"
 
 WHierarchicalTreeFibers::WHierarchicalTreeFibers() :
@@ -204,143 +202,3 @@ float WHierarchicalTreeFibers::getRatio( size_t cluster )
     }
     return static_cast<float>( fibersFromClusterActive ) / static_cast<float>( countFibersInCluster );
 }
-
-std::vector< size_t > WHierarchicalTreeFibers::findXBiggestClusters( size_t cluster, size_t number )
-{
-    //std::cout << number << " largest clusters for cluster: " << cluster << std::endl;
-
-    if ( number > m_containsLeafes[cluster].size() )
-    {
-        number = m_containsLeafes[cluster].size();
-    }
-
-    // init
-    std::list<size_t>worklist;
-    worklist.push_back( cluster );
-
-    while ( worklist.size() < number )
-    {
-        size_t current = worklist.front();
-        worklist.pop_front();
-        if ( m_containsLeafes[current].size() > 1 )
-        {
-            size_t left = m_children[current].first;
-            size_t right = m_children[current].second;
-            worklist.push_back( left );
-            worklist.push_back( right );
-        }
-        else
-        {
-            worklist.push_back( current );
-        }
-    }
-    sortList( worklist );
-
-    bool newSplit = true;
-
-    while ( newSplit )
-    {
-        newSplit = false;
-        size_t current = worklist.front();
-
-        if ( m_containsLeafes[current].size() > 1 )
-        {
-            size_t left = m_children[current].first;
-            size_t right = m_children[current].second;
-            size_t last = worklist.back();
-
-            if ( m_containsLeafes[left].size() > m_containsLeafes[last].size() )
-            {
-                worklist.pop_front();
-                worklist.push_back( left );
-                sortList( worklist );
-                newSplit = true;
-            }
-
-            last = worklist.back();
-            if ( m_containsLeafes[right].size() > m_containsLeafes[last].size() )
-            {
-                if ( !newSplit )
-                {
-                    worklist.pop_front();
-                }
-                if ( worklist.size() == number )
-                {
-                    worklist.pop_back();
-                }
-                worklist.push_back( right );
-                sortList( worklist );
-                newSplit = true;
-            }
-        }
-        sortList( worklist );
-    }
-
-    std::vector<size_t>returnVector;
-    std::list<size_t>::iterator it;
-    for ( it = worklist.begin(); it != worklist.end(); ++it )
-    {
-        size_t current = *it;
-        //std::cout << "cluster:" << current << "  size:" << m_containsLeafes[current].size() << std::endl;
-        returnVector.push_back( current );
-    }
-
-    return returnVector;
-}
-
-void WHierarchicalTreeFibers::sortList( std::list<size_t> &input ) //NOLINT
-{
-    if ( input.size() == 0 )
-    {
-        return;
-    }
-
-    std::vector<size_t>vec;
-    std::list<size_t>::iterator it;
-
-    for ( it = input.begin(); it != input.end(); ++it )
-    {
-        vec.push_back( *it );
-    }
-
-    for ( size_t n = vec.size() - 1; n > 0; --n )
-    {
-        for ( size_t i = 0; i < n; ++i )
-        {
-            if ( m_containsLeafes[vec[i]].size() < m_containsLeafes[vec[i+1]].size() )
-            {
-                size_t tmp = vec[i];
-                vec[i] = vec[i+1];
-                vec[i+1] = tmp;
-            }
-        }
-    }
-
-    input.clear();
-    for ( size_t k = 0; k < vec.size(); ++k )
-    {
-        input.push_back( vec[k] );
-    }
-}
-
-void WHierarchicalTreeFibers::colorCluster( size_t cluster, WColor color )
-{