[CHANGE] moved the fiber selector stuff to kernel to make it available for other modules

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"
 

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"

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/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

-//---------------------------------------------------------------------------
-//
-// 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/>.
-//
-//---------------------------------------------------------------------------
-
-#include <iostream>
-
-#include "../../graphicsEngine/WGEUtils.h"
-#include "WDendrogram.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 ) :
-    osg::Geode(),
-    m_tree( tree ),
-    m_rootCluster( cluster ),
-    m_minClusterSize( minClusterSize ),
-    m_xSize( xSize ),
-    m_ySize( ySize ),
-    m_xOff( xOffset ),
-    m_yOff( yOffset )
-{
-    create();
-}
-
-WDendrogram::~WDendrogram()
-{
-}
-
-void WDendrogram::create()
-{
-    m_colors = osg::ref_ptr<osg::Vec4Array>( new osg::Vec4Array );
-
-    m_vertexArray = new osg::Vec3Array;
-
-    m_lineArray = new osg::DrawElementsUInt( osg::PrimitiveSet::LINES, 0 );
-
-    float xMax = static_cast<float>( m_tree->size( m_rootCluster ) - 1 );
-    float yMax = m_tree->getLevel( m_rootCluster );
-
-    m_xMult = m_xSize / xMax;
-    m_yMult = m_ySize / yMax;
-
-    layout( m_rootCluster, 0.0f, static_cast<float>( m_tree->size( m_rootCluster ) - 1 ) );
-
-    for ( size_t i = 0; i < m_vertexArray->size(); ++i )
-    {
-        (*m_vertexArray)[i].x() = (*m_vertexArray)[i].x() * m_xMult + m_xOff;
-        (*m_vertexArray)[i].y() = (*m_vertexArray)[i].y() * m_yMult + m_yOff;
-    }
-
-    osg::ref_ptr< osg::Geometry > geometry = osg::ref_ptr< osg::Geometry >( new osg::Geometry() );
-
-    geometry->setVertexArray( m_vertexArray );
-
-    geometry->addPrimitiveSet( m_lineArray );
-
-    geometry->setColorArray( m_colors );
-    geometry->setColorBinding( osg::Geometry::BIND_PER_VERTEX );
-
-    osg::StateSet* state = geometry->getOrCreateStateSet();
-    state->setMode( GL_LIGHTING, osg::StateAttribute::OFF | osg::StateAttribute::PROTECTED );
-    addDrawable( geometry );
-}
-
-void WDendrogram::layout( size_t cluster, float left, float right )
-{
-    float height = m_tree->getLevel( cluster );
-
-    float size = right - left;
-
-    if ( m_tree->getLevel( cluster ) > 0 )
-    {
-        size_t leftCluster = m_tree->getChildren( cluster ).first;
-        size_t rightCluster = m_tree->getChildren( cluster ).second;
-
-        float leftHeight = m_tree->getLevel( leftCluster );
-        float leftSize = static_cast<float>( m_tree->size( leftCluster ) );
-
-        float rightHeight = m_tree->getLevel( rightCluster );
-        float rightSize = static_cast<float>( m_tree->size( rightCluster ) );
-
-        if ( ( leftSize >= m_minClusterSize ) &&  ( rightSize < m_minClusterSize ) )
-        //if ( rightSize < 2 )
-        {
-            // left cluster is much bigger, draw only left
-            m_vertexArray->push_back( osg::Vec3( ( left + size / 2.0 ), height, 0 ) );
-            m_vertexArray->push_back( osg::Vec3( ( left + size / 2.0 ), leftHeight, 0 ) );
-
-            m_lineArray->push_back( m_vertexArray->size() - 2 );
-            m_lineArray->push_back( m_vertexArray->size() - 1 );
-
-            m_colors->push_back( wge::osgColor( m_tree->getColor( cluster ) ) );
-            m_colors->push_back( wge::osgColor( m_tree->getColor( cluster ) ) );
-
-            layout( leftCluster, left, right );
-        }
-        else if ( ( rightSize >= m_minClusterSize ) &&  ( leftSize < m_minClusterSize ) )
-        //else if ( leftSize < 2 )
-        {
-            // right cluster is much bigger, draw only right
-            m_vertexArray->push_back( osg::Vec3( ( left + size / 2.0 ), height, 0 ) );
-            m_vertexArray->push_back( osg::Vec3( ( left + size / 2.0 ), rightHeight, 0 ) );
-
-            m_lineArray->push_back( m_vertexArray->size() - 2 );
-            m_lineArray->push_back( m_vertexArray->size() - 1 );
-
-            m_colors->push_back( wge::osgColor( m_tree->getColor( cluster ) ) );
-            m_colors->push_back( wge::osgColor( m_tree->getColor( cluster ) ) );
-
-            layout( rightCluster, left, right );
-        }
-        else
-        {
-            float mult = size / ( leftSize + rightSize );
-
-            m_vertexArray->push_back( osg::Vec3( ( left  + leftSize * mult  / 2.0 ), height, 0 ) );
-            m_vertexArray->push_back( osg::Vec3( ( right - rightSize * mult / 2.0 ), height, 0 ) );
-
-            m_lineArray->push_back( m_vertexArray->size() - 2 );
-            m_lineArray->push_back( m_vertexArray->size() - 1 );
-
-            m_vertexArray->push_back( osg::Vec3( ( left  + leftSize * mult  / 2.0 ), leftHeight, 0 ) );
-            m_vertexArray->push_back( osg::Vec3( ( right - rightSize * mult / 2.0 ), rightHeight, 0 ) );
-
-            m_colors->push_back( wge::osgColor( m_tree->getColor( cluster ) ) );
-            m_colors->push_back( wge::osgColor( m_tree->getColor( cluster ) ) );
-            m_colors->push_back( wge::osgColor( m_tree->getColor( cluster ) ) );
-            m_colors->push_back( wge::osgColor( m_tree->getColor( cluster ) ) );
-
-            m_lineArray->push_back( m_vertexArray->size() - 4 );
-            m_lineArray->push_back( m_vertexArray->size() - 2 );
-            m_lineArray->push_back( m_vertexArray->size() - 3 );
-            m_lineArray->push_back( m_vertexArray->size() - 1 );
-
-            layout( leftCluster, left, left + leftSize * mult );
-            layout( rightCluster, right - rightSize * mult, right );
-        }
-    }
-}
-
-size_t WDendrogram::getClickedCluster( int xClick, int yClick )
-{
-    m_xClicked = ( xClick - m_xOff ) / m_xSize * ( m_tree->size( m_rootCluster ) - 1 );
-    m_yClicked = ( yClick - m_yOff ) / m_ySize * ( m_tree->getLevel( m_rootCluster ) - 1 );
-
-    getClickClusterRecursive( m_rootCluster, 0.0f, static_cast<float>( m_tree->size( m_rootCluster ) - 1 ) );
-
-    //std::cout << xClick << "," << yClick << "  :  " << m_xClicked << "," << m_yClicked << std::endl;
-
-    return m_clickedCluster;
-}
-
-void WDendrogram::getClickClusterRecursive( size_t cluster, float left, float right )
-{
-    int height = m_tree->getLevel( cluster );
-
-    if ( height == m_yClicked )
-    {
-        m_clickedCluster = cluster;
-        return;
-    }
-
-    int size = right - left;
-
-    if ( m_tree->getLevel( cluster ) > 0 )
-    {
-        size_t leftCluster = m_tree->getChildren( cluster ).first;
-        size_t rightCluster = m_tree->getChildren( cluster ).second;
-
-        float leftSize = static_cast<float>( m_tree->size( leftCluster ) );
-        float rightSize = static_cast<float>( m_tree->size( rightCluster ) );
-
-        if ( ( leftSize >= m_minClusterSize ) &&  ( rightSize < m_minClusterSize ) )
-        {
-            // left cluster is much bigger, draw only left
-            getClickClusterRecursive( leftCluster, left, right );
-        }
-        else if ( ( rightSize >= m_minClusterSize ) &&  ( leftSize < m_minClusterSize ) )
-        {
-            // right cluster is much bigger, draw only right
-            getClickClusterRecursive( rightCluster, left, right );
-        }
-        else
-        {
-            float mult = size / ( leftSize + rightSize );
-
-            if ( m_xClicked < left + leftSize * mult )
-            {
-                getClickClusterRecursive( leftCluster, left, left + leftSize * mult );
-            }
-            else
-            {
-                getClickClusterRecursive( rightCluster, right - rightSize * mult, right );
-            }
-        }
-    }
-}

src/modules/clusterDisplay/WDendrogram.h

-//---------------------------------------------------------------------------
-//
-// 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/>.
-//
-//---------------------------------------------------------------------------
-
-#ifndef WDENDROGRAM_H
-#define WDENDROGRAM_H
-
-#include <osg/Geode>
-#include <osg/Vec3>
-#include <osg/Geometry>
-#include <osg/MatrixTransform>
-#include <osg/PositionAttitudeTransform>
-
-#include "WHierarchicalTree.h"
-
-/**
- * Class creates a dendrogram from a hierarchical clustering
- */
-class WDendrogram : public osg::Geode
-{
-public:
-    /**
-     * constructor
-     *
-     * \param tree reference to the tree object to work on
-     * \param cluster root cluster for the dendrogram
-     * \param minClusterSize minimum for cluster to be drawn, when i the whole tree is drawn
-     * \param xSize number of pixel to scale the tree on along the x axis
-     * \param ySize number of pixel to scale the tree on along the y axis
-     * \param xOffset translation alogn the x axis
-     * \param yOffset translation alogn the y axis
-     *
-     */
-    WDendrogram( WHierarchicalTree* tree, size_t cluster, size_t minClusterSize = 1, float xSize = 1000.f,
-            float ySize = 500.f, float xOffset = 0.0f, float yOffset = 0.0f );
-
-    /**
-     * destructor
-     */
-    ~WDendrogram();
-
-    /**
-     * calculate which cluster was clicked from given pixel coordinates
-     * \param xClick the x coordinate
-     * \param yClick the y coordinate
-     * \return the cluster id, will return the root cluster if no cluster can be determinded
-     */
-    size_t getClickedCluster( int xClick, int yClick );
-
-protected:
-private:
-    /**
-     * helper function the starts the layout process from the input data in the constructor
-     */
-    void create();
-
-    /**
-     * recursive funtion that lays out the tree from top to bottom
-     * \param cluster the current cluster to work on
-     * \param left left border of the current subcluster
-     * \param right right border of the current subcluster
-     */
-    void layout( size_t cluster, float left, float right );
-
-    /**
-     * recurse function that follows the layout to determine the cluster from pixel coordinates
-     *
-     * \param cluster cluster to check against coordinates
-     * \param left left boundary of cluster
-     * \param right right boundary of cluster
-     */
-    void getClickClusterRecursive( size_t cluster, float left, float right );
-
-    WHierarchicalTree* m_tree; //!< the tree to work on
-
-    size_t m_rootCluster; //!< top cluster to draw the tree from
-
-    osg::ref_ptr<osg::Vec4Array> m_colors; //!< color array
-
-    osg::Vec3Array* m_vertexArray; //!< vertex array
-
-    osg::DrawElementsUInt* m_lineArray; //!< line array
-
-    size_t m_minClusterSize; //!< minimum cluster size to be considered while laying out the dendrogram
-
-    float m_xSize; //!< x size in pixel of the final dendrogram
-    float m_ySize; //!< y size in pixel of the final dendrogram
-    float m_xOff; //!< x offset
-    float m_yOff; //!< y offset
-    float m_xMult; //!< helper variable for the recursive function
-    float m_yMult; //!< helper variable for the recursive function
-
-    int m_xClicked; //!< stores the click position for use int he recursive function
-    int m_yClicked; //!< stores the click position for use int he recursive function
-
-    size_t m_clickedCluster; //!< the clicked cluster
-};
-
-#endif  // WDENDROGRAM_H

src/modules/fiberDisplay/WFiberDrawable.h

@@ -35,7 +35,7 @@
 #include <osg/ShapeDrawable>
 #include <osg/Group>
 
-#include "WFiberSelector.h"
+#include "../../kernel/WFiberSelector.h"
 
 
 class WDataSetFibers;

src/modules/fiberDisplay/WMFiberDisplay.h

@@ -34,10 +34,10 @@
 #include "../../graphicsEngine/WROIBox.h"
 #include "../../graphicsEngine/WShader.h"
 
+#include "../../kernel/WFiberSelector.h"
 #include "../../kernel/WModule.h"
 #include "../../kernel/WModuleInputData.h"
 
-#include "WFiberSelector.h"
 #include "WFiberDrawable.h"
 
 /**