[MERGE]

doc/user/walnut.cfg.mpi

@@ -12,7 +12,7 @@ allowOnlyOneFiberDataSet = yes # This will prevent you from accidently loading m
 # 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,Mesh Reader,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
 
 ## 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

src/modules/fiberDisplay/WFiberDrawable.cpp → src/graphicsEngine/WFiberDrawable.cpp

@@ -24,8 +24,8 @@
 
 #include <vector>
 
-#include "../../dataHandler/WDataSetFibers.h"
-#include "../../kernel/WKernel.h"
+#include "../kernel/WKernel.h"
+
 #include "WFiberDrawable.h"
 
 // The constructor here does nothing. One thing that may be necessary is
@@ -35,9 +35,7 @@
 // time (that is, the vertices drawn change from time to time).
 WFiberDrawable::WFiberDrawable():
     osg::Drawable(),
-    m_useTubes( false ),
-    m_globalColoring( true ),
-    m_customColoring( false )
+    m_useTubes( false )
 {
     setSupportsDisplayList( false );
     // This contructor intentionally left blank. Duh.
@@ -85,35 +83,17 @@ void WFiberDrawable::drawImplementation( osg::RenderInfo& renderInfo ) const //N
 
 void WFiberDrawable::drawFibers( osg::RenderInfo& renderInfo ) const //NOLINT
 {
-    boost::shared_ptr< std::vector< size_t > > startIndexes = m_dataset->getLineStartIndexes();
-    boost::shared_ptr< std::vector< size_t > > pointsPerLine = m_dataset->getLineLengths();
-    boost::shared_ptr< std::vector< float > > verts = m_dataset->getVertices();
-    boost::shared_ptr< std::vector< float > > tangents = m_dataset->getTangents();
-
-    boost::shared_ptr< std::vector< float > > colors;
-
-    if ( m_customColoring )
-    {
-        colors = colors = m_dataset->getColorScheme( "Custom Color" )->getColor();
-    }
-    else
-    {
-        colors = ( m_globalColoring ? m_dataset->getGlobalColors() : m_dataset->getLocalColors() );
-    }
-
-    boost::shared_ptr< std::vector< bool > > active = m_fiberSelector->getBitfield();
-
     osg::State& state = *renderInfo.getState();
 
     state.disableAllVertexArrays();
-    state.setVertexPointer( 3, GL_FLOAT , 0, &( *verts )[0] );
-    state.setColorPointer( 3 , GL_FLOAT , 0, &( *colors )[0] );
-    state.setNormalPointer( GL_FLOAT , 0, &( *tangents )[0] );
-    for ( size_t i = 0; i < active->size(); ++i )
+    state.setVertexPointer( 3, GL_FLOAT , 0, &( *m_verts )[0] );
+    state.setColorPointer( 3 , GL_FLOAT , 0, &( *m_colors )[0] );
+    //state.setNormalPointer( GL_FLOAT , 0, &( *m_tangents )[0] );
+    for ( size_t i = 0; i < m_active->size(); ++i )
     {
-        if ( (*active)[i] )
+        if ( (*m_active)[i] )
         {
-            state.glDrawArraysInstanced( GL_LINE_STRIP, (*startIndexes)[i], (*pointsPerLine)[i], 1);
+            state.glDrawArraysInstanced( GL_LINE_STRIP, (*m_startIndexes)[i], (*m_pointsPerLine)[i], 1);
         }
     }
 
@@ -123,38 +103,20 @@ void WFiberDrawable::drawFibers( osg::RenderInfo& renderInfo ) const //NOLINT
 
 void WFiberDrawable::drawTubes() const
 {
-    boost::shared_ptr< std::vector< size_t > > startIndexes = m_dataset->getLineStartIndexes();
-    boost::shared_ptr< std::vector< size_t > > pointsPerLine = m_dataset->getLineLengths();
-    boost::shared_ptr< std::vector< float > > verts = m_dataset->getVertices();
-    boost::shared_ptr< std::vector< float > > tangents = m_dataset->getTangents();
-
-    boost::shared_ptr< std::vector< float > > colors;
-
-    if ( m_customColoring )
-    {
-        colors = m_dataset->getColorScheme( "Custom Color" )->getColor();
-    }
-    else
+    for( size_t i = 0; i < m_active->size(); ++i )
     {
-        colors = ( m_globalColoring ? m_dataset->getGlobalColors() : m_dataset->getLocalColors() );
-    }
-
-    boost::shared_ptr< std::vector< bool > > active = m_fiberSelector->getBitfield();
-
-    for( size_t i = 0; i < active->size(); ++i )
-    {
-        if ( active->at( i ) )
+        if ( (*m_active)[i] )
         {
             glBegin( GL_QUAD_STRIP );
-            int idx = startIndexes->at( i ) * 3;
-            for ( size_t k = 0; k < pointsPerLine->at( i ); ++k )
+            int idx = m_startIndexes->at( i ) * 3;
+            for ( size_t k = 0; k < m_pointsPerLine->at( i ); ++k )
             {
-                glNormal3f( tangents->at( idx ), tangents->at( idx + 1 ), tangents->at( idx + 2 ) );
-                glColor3f( colors->at( idx ), colors->at( idx + 1 ), colors->at( idx + 2 ) );
+                glNormal3f( m_tangents->at( idx ), m_tangents->at( idx + 1 ), m_tangents->at( idx + 2 ) );
+                glColor3f( m_colors->at( idx ), m_colors->at( idx + 1 ), m_colors->at( idx + 2 ) );
                 glTexCoord1f( -1.0f );
-                glVertex3f( verts->at( idx ), verts->at( idx + 1 ), verts->at( idx + 2 ) );
+                glVertex3f( m_verts->at( idx ), m_verts->at( idx + 1 ), m_verts->at( idx + 2 ) );
                 glTexCoord1f( 1.0f );
-                glVertex3f( verts->at( idx ), verts->at( idx + 1 ), verts->at( idx + 2 ) );
+                glVertex3f( m_verts->at( idx ), m_verts->at( idx + 1 ), m_verts->at( idx + 2 ) );
                 idx += 3;
                 //
             }
@@ -162,3 +124,8 @@ void WFiberDrawable::drawTubes() const
         }
     }
 }
+
+void WFiberDrawable::setDataset( boost::shared_ptr< const WDataSetFibers > dataset )
+{
+    m_dataset = dataset;
+}

src/modules/fiberDisplay/WFiberDrawable.h → src/graphicsEngine/WFiberDrawable.h

@@ -35,12 +35,8 @@
 #include <osg/ShapeDrawable>
 #include <osg/Group>
 
-#include "WFiberSelector.h"
-
-
-class WDataSetFibers;
 /**
- * TODO(schurade): Document this!
+ * Class implements an osg::Drawable that paints fiber representations either using lines or tubes
  */
 class WFiberDrawable: public osg::Drawable
 {
@@ -108,49 +104,46 @@ public:
     void setUseTubes( bool flag );
 
     /**
-     * Set the coloring modes of the fibers.
-     *
-     * \param globalColoring If true is given global coloring is applied ( default ), else local coloring
+     * Set the bounding box of all fibers.
+     * \param bb The new bounding box.
      */
-    void setColoringMode( bool globalColoring );
+    void setBoundingBox( const osg::BoundingBox & bb );
 
     /**
-     * Set the use of custom colors
-     *
-     * \param custom
+     * setter
+     * \param bitField selected fibers to draw
      */
-    void setCustomColoring( bool custom );
+    void setBitfield( boost::shared_ptr< std::vector< bool > > bitField );
 
     /**
-     * In which mode coloring for the fibers is applied.
-     *
-     * \return True for global, false for local coloring
+     * setter
+     * \param idx
      */
-    bool getColoringMode() const;
+    void setStartIndexes( boost::shared_ptr< std::vector< size_t > > idx );
 
     /**
-     * Set the bounding box of all fibers.
-     * \param bb The new bounding box.
+     * setter
+     * \param ppl
      */
-    void setBoundingBox( const osg::BoundingBox & bb );
+    void setPointsPerLine( boost::shared_ptr< std::vector< size_t > > ppl );
 
     /**
      * setter
-     * \param bitField selected fibers to draw
+     * \param verts
      */
-    void setBitfield( boost::shared_ptr< std::vector< bool > > bitField );
+    void setVerts( boost::shared_ptr< std::vector< float > > verts );
 
     /**
      * setter
-     * \param selector the selector object which provides the bitfield for fiber selection
+     * \param tangents
      */
-    void setSelector( boost::shared_ptr< WFiberSelector > selector );
+    void setTangents( boost::shared_ptr< std::vector< float > > tangents );
 
     /**
      * setter
-     * \param colors
+     * \param color
      */
-    void setCustomColors( boost::shared_ptr< std::vector< float > > colors );
+    void setColor( boost::shared_ptr< std::vector< float > > color );
 
 protected:
 private:
@@ -172,54 +165,53 @@ private:
 
     bool m_useTubes; //!< flag
 
-    bool m_globalColoring; //!< True indicates global, false local coloring
-
-    bool m_customColoring; //!< True indicates use of custom colors
-
-
     boost::shared_ptr< std::vector< bool > > m_active; //!< pointer to the bitfield of active fibers
 
-    boost::shared_ptr< WFiberSelector > m_fiberSelector; //!< the selector object which provides the bitfield for fiber selection
+    boost::shared_ptr< std::vector< size_t > > m_startIndexes; //!< pointer to the field of line start indexes
+    boost::shared_ptr< std::vector< size_t > > m_pointsPerLine; //!< pointer to the field of points per line
+    boost::shared_ptr< std::vector< float > > m_verts; //!< pointer to the field of vertexes
+    boost::shared_ptr< std::vector< float > > m_tangents; //!< pointer to the field of line tangents
+    boost::shared_ptr< std::vector< float > > m_colors; //!< pointer to the field of colors per vertex
 };
 
-inline void WFiberDrawable::setDataset( boost::shared_ptr< const WDataSetFibers > dataset )
+inline void WFiberDrawable::setUseTubes( bool flag )
 {
-    m_dataset = dataset;
+    m_useTubes = flag;
 }
 
-inline void WFiberDrawable::setUseTubes( bool flag )
+inline void WFiberDrawable::setBoundingBox( const osg::BoundingBox & bb )
 {
-    m_useTubes = flag;
+    setBound( bb );
 }
 
-inline void WFiberDrawable::setColoringMode( bool globalColoring )
+inline void WFiberDrawable::setBitfield( boost::shared_ptr< std::vector< bool > > bitField )
 {
-    m_globalColoring = globalColoring;
+    m_active = bitField;
 }
 
-inline bool WFiberDrawable::getColoringMode() const
+inline void WFiberDrawable::setStartIndexes( boost::shared_ptr< std::vector< size_t > > idx )
 {
-    return m_globalColoring;
+    m_startIndexes = idx;
 }
 
-inline void WFiberDrawable::setCustomColoring( bool custom )
+inline void WFiberDrawable::setPointsPerLine( boost::shared_ptr< std::vector< size_t > > ppl )
 {
-    m_customColoring = custom;
+    m_pointsPerLine = ppl;
 }
 
-inline void WFiberDrawable::setBoundingBox( const osg::BoundingBox & bb )
+inline void WFiberDrawable::setVerts( boost::shared_ptr< std::vector< float > > verts )
 {
-    setBound( bb );
+    m_verts = verts;
 }
 
-inline void WFiberDrawable::setBitfield( boost::shared_ptr< std::vector< bool > > bitField )
+inline void WFiberDrawable::setTangents( boost::shared_ptr< std::vector< float > > tangents )
 {
-    m_active = bitField;
+    m_tangents = tangents;
 }
 
-inline void WFiberDrawable::setSelector( boost::shared_ptr< WFiberSelector > selector )
+inline void WFiberDrawable::setColor( boost::shared_ptr< std::vector< float > > color )
 {
-    m_fiberSelector = selector;
+    m_colors = color;
 }
 
 #endif  // WFIBERDRAWABLE_H

src/modules/fiberDisplay/WFiberSelector.cpp → src/kernel/WFiberSelector.cpp

@@ -24,7 +24,7 @@
 
 #include <iostream>
 
-#include "../../kernel/WKernel.h"
+#include "../kernel/WKernel.h"
 
 #include "WFiberSelector.h"
 
@@ -136,28 +136,33 @@ void WFiberSelector::recalculate()
 {
     if ( m_branches.empty() )
     {
-        m_outputBitfield = boost::shared_ptr< std::vector< bool > >( new std::vector< bool >( m_size, true ) );
-        return;
+        m_workerBitfield = boost::shared_ptr< std::vector< bool > >( new std::vector< bool >( m_size, true ) );
     }
     else
     {
         m_workerBitfield = boost::shared_ptr< std::vector< bool > >( new std::vector< bool >( m_size, false ) );
-    }
-
-    for ( std::list< boost::shared_ptr< WSelectorBranch > >::iterator iter = m_branches.begin(); iter != m_branches.end(); ++iter )
-    {
-        boost::shared_ptr< std::vector< bool > > bf = ( *iter )->getBitField();
 
-        for ( size_t i = 0; i < m_size; ++i )
+        for ( std::list< boost::shared_ptr< WSelectorBranch > >::iterator iter = m_branches.begin(); iter != m_branches.end(); ++iter )
         {
-            ( *m_workerBitfield )[i] = ( *m_workerBitfield )[i] | ( *bf )[i];
+            boost::shared_ptr< std::vector< bool > > bf = ( *iter )->getBitField();
+
+            for ( size_t i = 0; i < m_size; ++i )
+            {
+                ( *m_workerBitfield )[i] = ( *m_workerBitfield )[i] | ( *bf )[i];
+            }
         }
     }
+
+    for ( size_t i = 0; i < m_size; ++i )
+    {
+      ( *m_outputBitfield )[i] = ( *m_workerBitfield )[i];
+    }
     m_dirty = false;
-    m_outputBitfield = m_workerBitfield;
+    //m_outputBitfield = m_workerBitfield;
 }
 
 void WFiberSelector::setDirty()
 {
+    recalculate();
     m_dirty = true;
 }

src/modules/fiberDisplay/WFiberSelector.h → src/kernel/WFiberSelector.h

@@ -28,7 +28,7 @@
 #include <list>
 #include <vector>
 
-#include "../../dataHandler/WDataSetFibers.h"
+#include "../dataHandler/WDataSetFibers.h"
 
 #include "WSelectorRoi.h"
 #include "WSelectorBranch.h"
@@ -102,20 +102,6 @@ protected:
      */
     void slotRemoveBranch( boost::shared_ptr< WRMBranch > branch );
 
-    /**
-     * setter
-     * \param colors
-     */
-    void setCustomColors( boost::shared_ptr< std::vector< float > > colors );
-
-    /**
-     * getter
-     * \return colors
-     */
-    boost::shared_ptr< std::vector< float > > getCustomColors();
-
-
-
 private:
     /**
      * update the bitfield when there was a change in the roi structure

src/modules/fiberDisplay/WKdTree.cpp → src/kernel/WKdTree.cpp

@@ -25,8 +25,8 @@
 #include <algorithm>
 #include <vector>
 
-#include "../../common/WAssert.h"
-#include "../../common/WLogger.h"
+#include "../common/WAssert.h"
+#include "../common/WLogger.h"
 
 #include "WKdTree.h"
 

src/modules/fiberDisplay/WKdTree.h → src/kernel/WKdTree.h

@@ -28,7 +28,7 @@
 #include <algorithm>
 #include <vector>
 
-#include "../../common/WThreadedRunner.h"
+#include "../common/WThreadedRunner.h"
 
 /**
  * implements the compare function for std::nth_element on a point array

src/kernel/WRMBranch.cpp

@@ -61,6 +61,9 @@ void WRMBranch::propertyChanged()
 void WRMBranch::addRoi( osg::ref_ptr< WROI > roi )
 {
     m_rois.push_back( roi );
+    boost::function< void() > changeRoiSignal = boost::bind( &WRMBranch::setDirty, this );
+    roi->addChangeNotifier( changeRoiSignal );
+
     setDirty();
 }
 

src/modules/fiberDisplay/WSelectorBranch.h → src/kernel/WSelectorBranch.h

@@ -29,7 +29,7 @@
 #include <vector>
 
 #include "WSelectorRoi.h"
-#include "../../kernel/WRMBranch.h"
+#include "../kernel/WRMBranch.h"
 
 /**
  * TODO(schurade): Document this!

src/modules/fiberDisplay/WSelectorRoi.cpp → src/kernel/WSelectorRoi.cpp

@@ -23,8 +23,8 @@
 //---------------------------------------------------------------------------
 
 //#include "../../../graphicsEngine/WGraphicsEngine.h"
-#include "../../graphicsEngine/WROIBox.h"
-#include "../../graphicsEngine/WROIArbitrary.h"
+#include "../graphicsEngine/WROIBox.h"
+#include "../graphicsEngine/WROIArbitrary.h"
 
 #include "WSelectorRoi.h"
 

src/modules/fiberDisplay/WSelectorRoi.h → src/kernel/WSelectorRoi.h

@@ -27,9 +27,9 @@
 
 #include <vector>
 
-#include "../../dataHandler/WDataSetFibers.h"
+#include "../dataHandler/WDataSetFibers.h"
 
-#include "../../graphicsEngine/WROI.h"
+#include "../graphicsEngine/WROI.h"
 
 #include "WKdTree.h"
 /**

src/modules/clusterDisplay/WDendrogram.cpp → src/modules/clusterDisplay/WDendrogramGeode.cpp

@@ -25,12 +25,13 @@
 #include <iostream>
 
 #include "../../graphicsEngine/WGEUtils.h"
-#include "WDendrogram.h"
+#include "WDendrogramGeode.h"
 
 /**
  * Class implements a dendrogram as an osg geode
  */
-WDendrogram::WDendrogram( WHierarchicalTree* tree, size_t cluster, size_t minClusterSize, float xSize, float ySize, float xOffset, float yOffset ) :
+WDendrogramGeode::WDendrogramGeode( WHierarchicalTree* tree, size_t cluster, size_t minClusterSize,
+                                    float xSize, float ySize, float xOffset, float yOffset ) :
     osg::Geode(),
     m_tree( tree ),
     m_rootCluster( cluster ),
@@ -43,11 +44,11 @@ WDendrogram::WDendrogram( WHierarchicalTree* tree, size_t cluster, size_t minClu
     create();
 }
 
-WDendrogram::~WDendrogram()
+WDendrogramGeode::~WDendrogramGeode()
 {
 }
 
-void WDendrogram::create()
+void WDendrogramGeode::create()
 {
     m_colors = osg::ref_ptr<osg::Vec4Array>( new osg::Vec4Array );