[MERGE] - merged default into gridChanges

src/common/WHierarchicalTree.cpp

@@ -119,96 +119,6 @@ std::vector< size_t > WHierarchicalTree::findXBiggestClusters( size_t cluster, s
     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 );
-        }
-    }
-
-    worklist.sort( compSize( this ) );
-
-    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 );
-
-                    worklist.sort( compSize( this ) );
-                    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 );
-
-                    worklist.sort( compSize( this ) );
-                    newSplit = true;
-                }
-            }
-        }
-    }
-
-    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 )

src/common/WHierarchicalTree.h

@@ -153,14 +153,6 @@ public:
      */
     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 );
-
     /**
      * sets the color for a selected cluster and all sub clusters
      * \param cluster

src/dataHandler/datastructures/WValueSetHistogram.cpp

@@ -254,10 +254,12 @@ std::ostream& operator<<( std::ostream& out, const WValueSetHistogram& h )
     {
         std::pair< double, double > interval = h.getIntervalForIndex( i );
         // NOTE: the notation for open intervals is [a,b) or alternatively [a,b[.
-        out << i << " = [" << interval.first << ", " << interval.second << ") = " << h[ i ] << std::endl;
+        //out << i << " = [" << interval.first << ", " << interval.second << ") = " << h[ i ] << std::endl;
+        out << interval.first << " " <<  interval.second << " " << std::min( h[ i ], size_t( 3000 ) ) << std::endl;
     }
     // the last interval is handled special
-    out << h.size() - 1 << " = [" << h.getIntervalForIndex( h.size() - 1 ).first << ", inf) = " << h[ h.size() - 1 ] << std::endl;
+    //out << h.size() - 1 << " = [" << h.getIntervalForIndex( h.size() - 1 ).first << ", inf) = " << h[ h.size() - 1 ] << std::endl;
+    out << h.getIntervalForIndex( h.size() - 1 ).first << " inf " << std::min( h[ h.size() - 1 ], size_t( 3000 ) ) << std::endl;
 
     return out;
 }

src/dataHandler/datastructures/WValueSetHistogram.h

@@ -270,12 +270,12 @@ inline size_t WValueSetHistogram::getIndexForValue( double value ) const
     // the position on the scala
     double pos = ( value - m_minimum ) / static_cast< double >( m_mappedBucketSize );
     // the index is the floor( position )
-    size_t idx = static_cast< size_t >( pos );
+    size_t idx = static_cast< size_t >( std::floor( pos ) );
 
     // is the index larger than the size?
     bool inU = ( idx < m_nMappedBuckets );
     // is the index smaller than the size?
-    bool inL = ( pos > 0.0 );
+    bool inL = ( pos >= 0.0 );
 
     // the trick done here is to clamp value into [m_minimum,m_maximum] without using if statements. The C++ Standard says that booleans are
     // always 1 if true.

src/graphicsEngine/algorithms/WMarchingLegoAlgorithm.cpp

@@ -399,9 +399,9 @@ boost::shared_ptr<WTriangleMesh> WMarchingLegoAlgorithm::genSurfaceOneValue( siz
         resultPos4D[3] = m_matrix( 3, 0 ) * pos[0] + m_matrix( 3, 1 ) * pos[1] + m_matrix( 3, 2 ) * pos[2] + m_matrix( 3, 3 ) * 1;
 
         ( *mapIterator ).second.newID = nextID;
-        triMesh->addVertex( resultPos4D[0] / resultPos4D[3] - 0.5,
-                            resultPos4D[1] / resultPos4D[3] - 0.5,
-                            resultPos4D[2] / resultPos4D[3] - 0.5 );
+        triMesh->addVertex( resultPos4D[0] / resultPos4D[3],
+                            resultPos4D[1] / resultPos4D[3],
+                            resultPos4D[2] / resultPos4D[3] );
         triMesh->addTextureCoordinate( texCoord );
         nextID++;
         mapIterator++;

src/graphicsEngine/algorithms/WMarchingLegoAlgorithm.h

@@ -253,9 +253,9 @@ template<typename T> boost::shared_ptr<WTriangleMesh> WMarchingLegoAlgorithm::ge
         resultPos4D[3] = m_matrix( 3, 0 ) * pos[0] + m_matrix( 3, 1 ) * pos[1] + m_matrix( 3, 2 ) * pos[2] + m_matrix( 3, 3 ) * 1;
 
         ( *mapIterator ).second.newID = nextID;
-        triMesh->addVertex( resultPos4D[0] / resultPos4D[3] - 0.5,
-                            resultPos4D[1] / resultPos4D[3] - 0.5,
-                            resultPos4D[2] / resultPos4D[3] - 0.5 );
+        triMesh->addVertex( resultPos4D[0] / resultPos4D[3],
+                            resultPos4D[1] / resultPos4D[3],
+                            resultPos4D[2] / resultPos4D[3] );
         triMesh->addTextureCoordinate( texCoord );
         nextID++;
         mapIterator++;

src/gui/qt4/controlPanel/WPropertyWidget.cpp

@@ -65,6 +65,10 @@ WPropertyWidget::WPropertyWidget(  boost::shared_ptr< WPropertyBase > property,
         setCurrentIndex( 1 );
     }
 
+    // if the property is hidden initially, hide widget too
+    setHidden( m_property->isHidden() );
+    m_label.setHidden( m_property->isHidden() );
+
     // setup the update callback
     m_connection = m_property->getUpdateCondition()->subscribeSignal( boost::bind( &WPropertyWidget::propertyChangeNotifier, this ) );
 }

src/gui/qt4/controlPanel/WQtControlPanel.cpp

@@ -804,8 +804,7 @@ void WQtControlPanel::selectDataModule( boost::shared_ptr< WDataSet > dataSet )
 
 WQtPropertyGroupWidget*  WQtControlPanel::buildPropWidget( boost::shared_ptr< WProperties > props )
 {
-    WQtPropertyGroupWidget* tab = new WQtPropertyGroupWidget( props->getName() );
-
+    WQtPropertyGroupWidget* tab = new WQtPropertyGroupWidget( props );
     if ( props.get() )
     {
         // read lock, gets unlocked upon destruction (out of scope)
@@ -816,47 +815,44 @@ WQtPropertyGroupWidget*  WQtControlPanel::buildPropWidget( boost::shared_ptr< WP
         // iterate all properties.
         for ( WProperties::PropertyConstIterator iter = propAccess->get().begin(); iter != propAccess->get().end(); ++iter )
         {
-            if ( !( *iter )->isHidden() )
+            switch ( ( *iter )->getType() )
             {
-                switch ( ( *iter )->getType() )
-                {
-                    case PV_BOOL:
-                        tab->addProp( ( *iter )->toPropBool() );
-                        break;
-                    case PV_INT:
-                        tab->addProp( ( *iter )->toPropInt() );
-                        break;
-                    case PV_DOUBLE:
-                        tab->addProp( ( *iter )->toPropDouble() );
-                        break;
-                    case PV_STRING:
-                        tab->addProp( ( *iter )->toPropString() );
-                        break;
-                    case PV_PATH:
-                        tab->addProp( ( *iter )->toPropFilename() );
-                        break;
-                    case PV_SELECTION:
-                        tab->addProp( ( *iter )->toPropSelection() );
-                        break;
-                    case PV_COLOR:
-                        tab->addProp( ( *iter )->toPropColor() );
-                        break;
-                    case PV_POSITION:
-                        tab->addProp( ( *iter )->toPropPosition() );
-                        break;
-                    case PV_TRIGGER:
-                        tab->addProp( ( *iter )->toPropTrigger() );
-                        break;
-                    case PV_GROUP:
-                        tab->addGroup( buildPropWidget( ( *iter )->toPropGroup() ) );
-                        break;
-                    case PV_MATRIX4X4:
-                        tab->addProp( ( *iter )->toPropMatrix4X4() );
-                        break;
-                    default:
-                        WLogger::getLogger()->addLogMessage( "This property type is not yet supported.", "ControlPanel", LL_WARNING );
-                        break;
-                }
+                case PV_BOOL:
+                    tab->addProp( ( *iter )->toPropBool() );
+                    break;
+                case PV_INT:
+                    tab->addProp( ( *iter )->toPropInt() );
+                    break;
+                case PV_DOUBLE:
+                    tab->addProp( ( *iter )->toPropDouble() );
+                    break;
+                case PV_STRING:
+                    tab->addProp( ( *iter )->toPropString() );
+                    break;
+                case PV_PATH:
+                    tab->addProp( ( *iter )->toPropFilename() );
+                    break;
+                case PV_SELECTION:
+                    tab->addProp( ( *iter )->toPropSelection() );
+                    break;
+                case PV_COLOR:
+                    tab->addProp( ( *iter )->toPropColor() );
+                    break;
+                case PV_POSITION:
+                    tab->addProp( ( *iter )->toPropPosition() );
+                    break;
+                case PV_TRIGGER:
+                    tab->addProp( ( *iter )->toPropTrigger() );
+                    break;
+                case PV_GROUP:
+                    tab->addGroup( buildPropWidget( ( *iter )->toPropGroup() ) );
+                    break;
+                case PV_MATRIX4X4:
+                    tab->addProp( ( *iter )->toPropMatrix4X4() );
+                    break;
+                default:
+                    WLogger::getLogger()->addLogMessage( "This property type is not yet supported.", "ControlPanel", LL_WARNING );
+                    break;
             }
         }
     }

src/gui/qt4/controlPanel/WQtPropertyGroupWidget.cpp

@@ -24,18 +24,45 @@
 
 #include <string>
 
+#include <QtGui/QApplication>
 #include <QtGui/QGroupBox>
 #include <QtGui/QPushButton>
 #include <QtGui/QScrollArea>
 
+#include "../events/WEventTypes.h"
+#include "../events/WPropertyChangedEvent.h"
+
+#include "../../../common/WProperties.h"
+
 #include "WQtPropertyGroupWidget.h"
 
+WQtPropertyGroupWidget::WQtPropertyGroupWidget( WPropGroup group, QWidget* parent )
+    : QWidget( parent ),
+    m_name( group->getName().c_str() ),
+    m_numberOfWidgets( 0 ),
+    m_group( group )
+{
+    // note: never do layouts as none pointers
+    // on destruction of a widget it will try to delete them which will cause crashes
+    m_pageLayout = new QVBoxLayout();
+    m_controlLayout = new QGridLayout();
+    m_pageLayout->addLayout( m_controlLayout );
+
+    // NOTE: a simple setHidden( group->isHidden() ) causes the QWidgets to popup if hidden is false. This is why we set hidden only if it really
+    // is needed
+    if ( group->isHidden() )
+    {
+        setHidden( true );
+    }
+    // setup the update callback
+    m_connection = m_group->getUpdateCondition()->subscribeSignal( boost::bind( &WQtPropertyGroupWidget::propertyChangeNotifier, this ) );
+}
+
 WQtPropertyGroupWidget::WQtPropertyGroupWidget( std::string name, QWidget* parent  )
     : QWidget( parent ),
     m_name( name.c_str() ),
-//    m_controlLayout(),
-//    m_pageLayout(),
-    m_numberOfWidgets( 0 )
+    m_numberOfWidgets( 0 ),
+    m_group()
 {
     // note: never do layouts as none pointers
     // on destruction of a widget it will try to delete them which will cause crashes
@@ -46,6 +73,26 @@ WQtPropertyGroupWidget::WQtPropertyGroupWidget( std::string name, QWidget* paren
 
 WQtPropertyGroupWidget::~WQtPropertyGroupWidget()
 {
+    // cleanup
+    m_connection.disconnect();
+}
+
+void WQtPropertyGroupWidget::propertyChangeNotifier()
+{
+    QCoreApplication::postEvent( this, new WPropertyChangedEvent() );
+}
+
+bool WQtPropertyGroupWidget::event( QEvent* event )
+{
+    // a property changed
+    if ( event->type() == WQT_PROPERTY_CHANGED_EVENT )
+    {
+        setHidden( m_group->isHidden() );
+        emit hideSignal( m_group->isHidden() );
+        return true;
+    }
+
+    return QWidget::event( event );
 }
 
 WPropertyBoolWidget* WQtPropertyGroupWidget::addProp( WPropBool property )
@@ -177,6 +224,10 @@ void WQtPropertyGroupWidget::addGroup( WQtPropertyGroupWidget* widget, bool asSc
     // insert into layout
     int row = m_controlLayout->rowCount();
     m_controlLayout->addWidget( box, row, 0, 1, 2 );
+
+    // hide the box too if the property gets hidden
+    box->setHidden( widget->isHidden() );
+    connect( widget, SIGNAL( hideSignal( bool ) ), box, SLOT( setHidden( bool ) ) );
 }
 
 void WQtPropertyGroupWidget::addSpacer()

src/gui/qt4/controlPanel/WQtPropertyGroupWidget.h

@@ -51,12 +51,19 @@ class WQtPropertyGroupWidget : public QWidget
     Q_OBJECT
 
 public:
+    /**
+     * Creates new widget for a property group. Use this constructor to provide automatic hidden-flag management.
+     * \param group The group
+     * \param parent The widget managing this widget
+     */
+    WQtPropertyGroupWidget( WPropGroup group, QWidget* parent = 0 );
+
     /**
      * Creates new widget for a property group
      * \param name Name of the widget
      * \param parent The widget managing this widget
      */
-    explicit WQtPropertyGroupWidget( std::string name, QWidget* parent = 0 );
+    WQtPropertyGroupWidget( std::string name, QWidget* parent = 0 );
 
     /**
      * destructor
@@ -191,7 +198,33 @@ public:
      */
     void setName( QString name );
 
+signals:
+
+    /**
+     * A Signal which gets emitted whenever the widget should be hidden. This is a useful signal for containers which embed this group.
+     *
+     * \param hide if true, the widget should be hidden.
+     */
+    void hideSignal( bool hide );
+
 protected:
+
+    /**
+     * Callback for WPropertyBase::getChangeCondition. It emits an event to ensure all updates are done in gui thread.
+     */
+    virtual void propertyChangeNotifier();
+
+    /**
+     * Custom event dispatcher. Gets called by QT's Event system every time an event got sent to this widget. This event handler
+     * processes property change events.
+     *
+     * \note QT Doc says: use event() for custom events.
+     * \param event the event that got transmitted.
+     *
+     * \return true if the event got handled properly.
+     */
+    virtual bool event( QEvent* event );
+
 private:
 
     /**
@@ -213,6 +246,16 @@ private:
      * The number of widgets inside this one.
      */
     unsigned int m_numberOfWidgets;
+
+    /**
+     * The property group handled here.
+     */
+    WPropGroup m_group;
+
+    /**
+     * The connection for propertyChangeNotifier().
+     */
+    boost::signals2::connection m_connection;
 };
 
 #endif  // WQTPROPERTYGROUPWIDGET_H

src/modules/clusterDisplayVoxels/WMClusterDisplayVoxels.h

@@ -35,6 +35,7 @@
 #include "../../dataHandler/WDataHandler.h"
 #include "../../dataHandler/WDataSetScalar.h"
 #include "../../dataHandler/WDataTexture3D.h"
+#include "../../graphicsEngine/WGETexture.h"
 #include "../../dataHandler/WSubject.h"
 #include "../../dataHandler/WValueSet.h"
 #include "../../graphicsEngine/geodes/WDendrogramGeode.h"
@@ -186,6 +187,17 @@ private:
      */
     void dendrogramClick( WPickInfo pickInfo );
 
+    /**
+     * update the output connector on demand, for performance reasons this is not done every time
+     * a change to the cluster selection is applied
+     */
+    void updateOutDataset();
+
+    /**
+     * helper function to set the label on the in scene buttons depending on which labeling scheme is selected
+     */
+    void setButtonLabels();
+
 
     /**
      * An input connector that accepts order 1 datasets.
@@ -217,6 +229,12 @@ private:
      */
     osg::ref_ptr<osg::Texture3D>m_texture;
 
+    /**
+     * stores a pointer to the texture we paint in
+     */
+//    osg::ref_ptr< WGETexture3D > m_texture;
+
+
     /**
      * label vector for texture creation
      */
@@ -316,12 +334,6 @@ private:
      */
     WPropGroup m_groupTriangulation;
 
-
-    /**
-     * grouping the properties controlling cluster selection for minimum branch length
-     */
-    WPropGroup m_groupMinBranchLength;
-
     /**
      * controls the display of the dendrogram overlay
      */
@@ -394,6 +406,36 @@ private:
     WPropInt m_infoMaxLevel; //!< info property
 
     std::vector< std::vector<size_t> >m_loadedPartitions; //!< set partitions loaded from file
+
+    /**
+     * updates the output connector on demand, as we don't want to do this every paint command
+     */
+    WPropTrigger m_buttonUpdateOutput;
+
+    /**
+     * A list of cluster selection methods
+     */
+    boost::shared_ptr< WItemSelection > m_clusterSelectionsList;
+
+    /**
+     * Selection property for clusters
+     */
+    WPropSelection m_clusterSelection;
+
+    /**
+     * triggers the cluster selection update
+     */
+    WPropTrigger m_buttonExecuteSelection;
+
+    /**
+     * A list of button labels
+     */
+    boost::shared_ptr< WItemSelection > m_buttonLabelList;
+
+    /**
+     * Selection property for button labels
+     */
+    WPropSelection m_buttonLabelSelection;
 };
 
 #endif  // WMCLUSTERDISPLAYVOXELS_H

src/modules/histogramEqualization/WMHistogramEqualization.cpp

@@ -23,6 +23,7 @@
 //---------------------------------------------------------------------------
 
 #include <vector>
+#include <fstream>
 #include <string>
 
 #include "../../kernel/WKernel.h"
@@ -211,16 +212,21 @@ void WMHistogramEqualization::moduleMain()
                 curI++;
             }
 
-            debugLog() << "Clamped " << perc << "% resulting in new interval ["<< lower << ", " << upper <<").";
+            debugLog() << "Clamped " << perc << "% of [" << hist->getMinimum() << ", " << hist->getMaximum() << "]" <<
+                          " resulting in new interval [" << lower << ", " << upper <<").";
 
             // with this new interval, extract a new histogram and use it for equalization
             hist = boost::shared_ptr< const WValueSetHistogram >( new WValueSetHistogram( valueSet, lower, upper, cdfHistRes ) );
         }
 
         // the new data
-        std::vector< unsigned char > newData;
+        std::vector< double > newData;
         newData.resize( hist->getTotalElementCount(), 0 );
 
+        // these values are needed to rescale the data to the original interval
+        double valueMin = hist->getMinimum();
+        double valueScaler = hist->getMaximum() - valueMin;
+
         // equalize?
         ++*progress;
         if ( m_equalize->get( true ) )
@@ -232,24 +238,23 @@ void WMHistogramEqualization::moduleMain()
 
             // go through each CDF item and fill it, which is the sum of all previous items in hist
             size_t accum = 0;
+            double cdfMin = ( *hist )[ 0 ];
+            double cdfScaler = static_cast< double >( valueSet->rawSize() ) - cdfMin;
             for( size_t i = 0; i < hist->size(); ++i )
             {
                 // the CDF at i is the summed up histogram from 0 to i
                 // we additionally require the histogram to be normalized so divide by the total count
                 accum += ( *hist )[ i ];
-                cdf[ i ] = accum;
+                cdf[ i ] = accum - cdfMin;
             }
 
             // finally, build the new dataset
             debugLog() << "Calculating equalized value-set";
-            double cdfMin = cdf[ 0 ];
             for ( size_t vi = 0; vi < valueSet->rawSize(); ++vi )
             {
-                double cdfVI = cdf[ hist->getIndexForValue( valueSet->getScalarDouble( vi ) ) ];
-
-                newData[ vi ] = static_cast< unsigned char >(
-                        255.0 * ( cdfVI - cdfMin ) / (  static_cast< double >( valueSet->rawSize() ) - cdfMin )
-                );
+                size_t idx = hist->getIndexForValue( valueSet->getScalarDouble( vi ) );
+                double cdfVI = cdf[ idx ];
+                newData[ vi ] = valueMin + ( valueScaler * cdfVI / cdfScaler );
             }
         }
         else
@@ -260,7 +265,8 @@ void WMHistogramEqualization::moduleMain()
             for ( size_t vi = 0; vi < valueSet->rawSize(); ++vi )
             {