[ADD #157] checked that the fiber clustering really works and now it displays...

[ADD #157] checked that the fiber clustering really works and now it displays also some fibers... this is just a proof of concept hack ATM! So do not relay on that

src/modules/fiberClustering/WFiberCluster.h

@@ -62,9 +62,9 @@ public:
     void merge( WFiberCluster &other ); // NOLINT
 
     /**
-     * Returns a copy of all indices inside this cluster
+     * Returns a const reference of all indices inside this cluster
      */
-    const std::list< size_t > getIndices() const;
+    const std::list< size_t >& getIndices() const;
 
     /**
      * Find the minimal distance for any pair of fibers where one fiber is
@@ -181,7 +181,7 @@ inline bool WFiberCluster::operator!=( const WFiberCluster& other ) const
     return m_memberIndices != other.m_memberIndices;
 }
 
-inline const std::list< size_t > WFiberCluster::getIndices() const
+inline const std::list< size_t >& WFiberCluster::getIndices() const
 {
     return m_memberIndices;
 }

src/modules/fiberClustering/WMFiberClustering.cpp

@@ -25,6 +25,7 @@
 #include <algorithm>
 #include <iomanip>
 #include <iostream>
+#include <list>
 #include <string>
 #include <vector>
 
@@ -37,6 +38,7 @@
 #include "../../common/WColor.h"
 #include "../../common/WLogger.h"
 #include "../../common/WStatusReport.h"
+#include "../../common/WStringUtils.hpp"
 #include "../../dataHandler/WDataHandler.h"
 #include "../../dataHandler/WSubject.h"
 #include "../../dataHandler/WDataSetFibers.h"
@@ -122,6 +124,11 @@ void WMFiberClustering::cluster()
     {
         m_dLtTable.reset( new WDXtLookUpTable( numFibers ) );
     }
+    m_proximity_t = 1.0;
+    std::cout << "Proximity threshold: " << m_proximity_t << std::endl;
+    m_maxDistance_t = 6.5;
+    std::cout << "Maximum inter cluster distance threshold: " << m_maxDistance_t << std::endl;
+    WStatusReport st( numFibers );
 
     WDLTMetric dLt( m_proximity_t * m_proximity_t );  // metric instance for computation of the dLt measure
     for( size_t i = 0; i < numFibers; ++i )  // loop over all "symmetric" fibers pairs
@@ -159,7 +166,10 @@ void WMFiberClustering::cluster()
                 }
             }
         }
+        std::cout << "\r" << std::fixed << std::setprecision( 2 );
+        std::cout << ( ++st ).progress() << " " << st.stringBar() << std::flush;
     }
+    std::cout << std::endl;
     m_dLtTableExists = true;
 
     // remove empty clusters
@@ -187,6 +197,49 @@ void WMFiberClustering::cluster()
     m_lastFibsSize = m_fibs->size();
 }
 
+osg::ref_ptr< osg::Geode > WMFiberClustering::genFiberGeode( const WFiberCluster &cluster, const WColor color ) const
+{
+    using osg::ref_ptr;
+    ref_ptr< osg::Vec3Array > vertices = ref_ptr< osg::Vec3Array >( new osg::Vec3Array );
+    ref_ptr< osg::Geometry > geometry = ref_ptr< osg::Geometry >( new osg::Geometry );
+
+    std::list< size_t >::const_iterator cit = cluster.getIndices().begin();
+    for( ; cit !=  cluster.getIndices().end(); ++cit )
+    {
+        const wmath::WFiber &fib = (*m_fibs)[ *cit ];
+        for( size_t i = 0; i < fib.size(); ++i )
+        {
+            vertices->push_back( osg::Vec3( fib[i][0], fib[i][1], fib[i][2] ) );
+        }
+        geometry->addPrimitiveSet( new osg::DrawArrays( osg::PrimitiveSet::LINE_STRIP, vertices->size() - fib.size(), fib.size() ) );
+    }
+
+    geometry->setVertexArray( vertices );
+
+    ref_ptr< osg::Vec4Array > colors = ref_ptr< osg::Vec4Array >( new osg::Vec4Array );
+    colors->push_back( color.getOSGColor() );
+    geometry->setColorArray( colors );
+    geometry->setColorBinding( osg::Geometry::BIND_OVERALL );
+
+    osg::ref_ptr< osg::Geode > geode = osg::ref_ptr< osg::Geode >( new osg::Geode );
+    geode->addDrawable( geometry.get() );
+    return geode;
+}
+
+
 void WMFiberClustering::paint()
 {
+    double hue = 0.0;
+    double hue_increment = 1.0 / m_clusters.size();
+    WColor color;
+
+    std::cout << "cluster: " << m_clusters.size() << std::endl;
+    osg::ref_ptr< osg::Group > group = osg::ref_ptr< osg::Group >( new osg::Group );
+    for( size_t i = 0; i < m_clusters.size(); ++i, hue += hue_increment )
+    {
+        color.setHSV( hue, 1.0, 0.75 );
+        group->addChild( genFiberGeode( m_clusters[i], color ).get() );
+    }
+    group->getOrCreateStateSet()->setMode( GL_LIGHTING, osg::StateAttribute::OFF );
+    WKernel::getRunningKernel()->getGraphicsEngine()->getScene()->addChild( group.get() );
 }

src/modules/fiberClustering/WMFiberClustering.h

@@ -87,6 +87,8 @@ private:
      */
     void cluster();
 
+    osg::ref_ptr< osg::Geode > genFiberGeode( const WFiberCluster &cluster, const WColor color ) const;
+
     /**
      * Choose colors and build and commit new FgePrimitve
      */
@@ -149,7 +151,7 @@ private:
 
 inline const std::string WMFiberClustering::getName() const
 {
-    return std::string( "FiberClustering" );
+    return std::string( "Fiber Clustering Module" );
 }
 
 inline const std::string WMFiberClustering::getDescription() const

src/modules/fiberCulling/WMFiberCulling.cpp

@@ -109,7 +109,10 @@ void WMFiberCulling::cullOutFibers( boost::shared_ptr< WDataSetFibers > fibers )
 
     fibers->sortDescLength();  // sort the fiber on their length (biggest first)
     std::cout << "Sorted fibers done." << std::endl;
-
+    m_proximity_t = 1.0;
+    std::cout << "Proximity threshold: " << m_proximity_t << std::endl;
+    m_dSt_culling_t = 6.5;
+    std::cout << "Culling threshold: " << m_dSt_culling_t << std::endl;
     std::vector< bool > unusedFibers( numFibers, false );
     WDSTMetric dSt( m_proximity_t * m_proximity_t );
     WStatusReport st( numFibers );

src/modules/fiberCulling/WMFiberCulling.h

@@ -104,7 +104,7 @@ private:
 
 inline const std::string WMFiberCulling::getName() const
 {
-    return std::string( "FiberCulling" );
+    return std::string( "Fiber Culling Module" );
 }
 
 inline const std::string WMFiberCulling::getDescription() const

src/modules/fiberDisplay/WMFiberDisplay.cpp

@@ -96,26 +96,55 @@ osg::ref_ptr< osg::Geode > WMFiberDisplay::genFiberGeode(
 
 void WMFiberDisplay::moduleMain()
 {
-    ready();
-    while( !m_FinishRequested )
+//    ready();
+//    while( !m_FinishRequested )
+//    {
+//        if( m_fiberInput->getData() != boost::shared_ptr< const WDataSetFibers >() )
+//        {
+//            boost::shared_ptr< const WDataSetFibers > fiberDS = m_fiberInput->getData();
+//
+//            osg::ref_ptr< osg::Group > group = osg::ref_ptr< osg::Group >( new osg::Group );
+//            group->addChild( genFiberGeode( fiberDS, false ).get() );
+//            group->getOrCreateStateSet()->setMode( GL_LIGHTING, osg::StateAttribute::OFF );
+//
+//            WKernel::getRunningKernel()->getGraphicsEngine()->getScene()->addChild( group.get() );
+//        }
+//        // TODO(math): implement some redraw if data has changed
+//        //  - replacing the OSG group node?
+//        //  - using notifyDataChange() method
+//        while( !m_FinishRequested )
+//        {
+//            sleep( 1 );
+//        }
+//    }
+    boost::shared_ptr< WDataHandler > dataHandler;
+    // TODO(math): fix this hack when possible by using an input connector.
+    while( !WKernel::getRunningKernel() )
     {
-        if( m_fiberInput->getData() != boost::shared_ptr< const WDataSetFibers >() )
-        {
-            boost::shared_ptr< const WDataSetFibers > fiberDS = m_fiberInput->getData();
+        sleep( 1 );
+    }
+    while( !( dataHandler = WKernel::getRunningKernel()->getDataHandler() ) )
+    {
+        sleep( 1 );
+    }
+    while( !dataHandler->getNumberOfSubjects() )
+    {
+        sleep( 1 );
+    }
 
-            osg::ref_ptr< osg::Group > group = osg::ref_ptr< osg::Group >( new osg::Group );
-            group->addChild( genFiberGeode( fiberDS, false ).get() );
-            group->getOrCreateStateSet()->setMode( GL_LIGHTING, osg::StateAttribute::OFF );
+    boost::shared_ptr< const WDataSetFibers > fiberDS;
+    assert( fiberDS = boost::shared_dynamic_cast< const WDataSetFibers >( dataHandler->getSubject( 0 )->getDataSet( 0 ) ) );
+    osg::ref_ptr< osg::Group > group = osg::ref_ptr< osg::Group >( new osg::Group );
+    group->addChild( genFiberGeode( fiberDS, false ).get() );
+    group->getOrCreateStateSet()->setMode( GL_LIGHTING, osg::StateAttribute::OFF );
 
-            WKernel::getRunningKernel()->getGraphicsEngine()->getScene()->addChild( group.get() );
-        }
-        // TODO(math): implement some redraw if data has changed
-        //  - replacing the OSG group node?
-        //  - using notifyDataChange() method
-        while( !m_FinishRequested )
-        {
-            sleep( 1 );
-        }
+    WKernel::getRunningKernel()->getGraphicsEngine()->getScene()->addChild( group.get() );
+
+    // Since the modules run in a separate thread: such loops are possible
+    while ( !m_FinishRequested )
+    {
+        // do fancy stuff
+        sleep( 1 );
     }
 }