[MERGE]

src/graphicsEngine/WTriangleMesh2.cpp

@@ -185,6 +185,12 @@ osg::Vec3 WTriangleMesh2::getVertex( size_t index ) const
     return ( *m_verts )[index];
 }
 
+osg::Vec4 WTriangleMesh2::getVertColor( size_t index ) const
+{
+    WAssert( index < m_countVerts, "get vertex: index out of range" );
+    return ( *m_vertColors )[index];
+}
+
 wmath::WPosition WTriangleMesh2::getVertexAsPosition( size_t index ) const
 {
     WAssert( index < m_countVerts, "get vertex as position: index out of range" );
@@ -389,6 +395,10 @@ void WTriangleMesh2::doLoopSubD()
     }
 
     delete[] newVertexPositions;
+
+    ( *m_vertNormals ).resize( ( *m_verts ).size() );
+    ( *m_vertColors ).resize( ( *m_verts ).size() );
+
     m_meshDirty = true;
 }
 
@@ -565,6 +575,44 @@ size_t WTriangleMesh2::loopGetThirdVert( size_t coVert1, size_t coVert2, size_t
     return getTriVertId2( triangleNum );
 }
 
+void WTriangleMesh2::addMesh( boost::shared_ptr<WTriangleMesh2> mesh, float xOff, float yOff, float zOff )
+{
+    size_t oldVertSize = m_countVerts;
+
+    ( *m_vertColors ).resize( oldVertSize + mesh->vertSize() );
+    for ( size_t i = 0; i < mesh->vertSize(); ++i )
+    {
+        osg::Vec3 v( mesh->getVertex( i ) );
+        v[0] += xOff;
+        v[1] += yOff;
+        v[2] += zOff;
+        addVertex( v );
+        setVertexColor( oldVertSize + i, mesh->getVertColor( i ) );
+    }
+    for ( size_t i = 0; i < mesh->triangleSize(); ++i )
+    {
+        addTriangle( mesh->getTriVertId0( i ) + oldVertSize, mesh->getTriVertId1( i ) + oldVertSize, mesh->getTriVertId2( i ) + oldVertSize );
+    }
+    m_meshDirty = true;
+}
+
+void WTriangleMesh2::translateMesh( float xOff, float yOff, float zOff )
+{
+    osg::Vec3 t( xOff, yOff, zOff );
+    for ( size_t i = 0; i < ( *m_verts ).size(); ++i )
+    {
+        ( *m_verts )[i] += t;
+    }
+}
+
+void WTriangleMesh2::zoomMesh( float zoom )
+{
+    for ( size_t i = 0; i < ( *m_verts ).size(); ++i )
+    {
+        ( *m_verts )[i] *= zoom;
+    }
+}
+
 std::ostream& tm_utils::operator<<( std::ostream& os, const WTriangleMesh2& rhs )
 {
     std::stringstream ss;

src/graphicsEngine/WTriangleMesh2.h

@@ -126,6 +126,14 @@ public:
      */
     void addTriangle( osg::Vec3 vert0, osg::Vec3 vert1, osg::Vec3 vert2 );
 
+    /**
+     * sets a vertex to a new position
+     *
+     * \param index
+     * \param vert
+     */
+    void setVertex( size_t index, osg::Vec3 vert );
+
     /**
      * sets the normal for a given vertex
      *
@@ -218,6 +226,14 @@ public:
      */
     osg::Vec3 getVertex( size_t index ) const;
 
+    /**
+     * getter
+     *
+     * \param index
+     * \return color
+     */
+    osg::Vec4 getVertColor( size_t index ) const;
+
     /**
      * getter
      *
@@ -287,6 +303,32 @@ public:
      */
     size_t getTriVertId2( size_t triId ) const;
 
+    /**
+     *  adds a mesh to the existing, no check for duplicate vertexes is performed, an additional
+     *  vector may be specified to move the mesh to add
+     *
+     *  \param mesh
+     *  \param xOff
+     *  \param yOff
+     *  \param zOff
+     */
+    void addMesh( boost::shared_ptr<WTriangleMesh2> mesh, float xOff = 0., float yOff = 0., float zOff = 0. );
+
+    /**
+     *  moves the entire mesh to a new postion
+     *
+     *  \param xOff
+     *  \param yOff
+     *  \param zOff
+     */
+    void translateMesh( float xOff, float yOff, float zOff );
+
+    /**
+     * multiplies the vertex vectors of the mesh with a given number
+     *
+     * \param zoom
+     */
+    void zoomMesh( float zoom );
 
 protected:
     static boost::shared_ptr< WPrototyped > m_prototype; //!< The prototype as singleton.
@@ -586,4 +628,9 @@ inline size_t WTriangleMesh2::getTriVertId2( size_t triId ) const
     return m_triangles[triId * 3 + 2];
 }
 
+inline void WTriangleMesh2::setVertex( size_t index, osg::Vec3 vert )
+{
+    ( *m_verts )[index] = vert;
+}
+
 #endif  // WTRIANGLEMESH2_H

src/kernel/WModuleFactory.cpp

@@ -54,6 +54,7 @@
 #include "../modules/triangleMeshRenderer/WMTriangleMeshRenderer.h"
 #include "../modules/writeNIfTI/WMWriteNIfTI.h"
 #include "../modules/vectorPlot/WMVectorPlot.h"
+#include "../modules/geometryGlyphs/WMGeometryGlyphs.h"
 #include "WModuleFactory.h"
 #include "exceptions/WPrototypeNotUnique.h"
 #include "exceptions/WPrototypeUnknown.h"
@@ -108,6 +109,7 @@ void WModuleFactory::load()
     m_prototypes.insert( boost::shared_ptr< WModule >( new WMSurfaceParticles() ) );
     m_prototypes.insert( boost::shared_ptr< WModule >( new WMClusterSlicer() ) );
     m_prototypes.insert( boost::shared_ptr< WModule >( new WMVectorPlot() ) );
+    m_prototypes.insert( boost::shared_ptr< WModule >( new WMGeometryGlyphs() ) );
 
     lock.unlock();
 

src/modules/geometryGlyphs/WMGeometryGlyphs.cpp

+//---------------------------------------------------------------------------
+//
+// Project: OpenWalnut ( http://www.openwalnut.org )
+//
+// Copyright 2009 OpenWalnut Community, BSV-Leipzig and CNCF-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 <string>
+#include <vector>
+
+#include <osg/Geode>
+#include <osg/Geometry>
+#include <osg/Material>
+#include <osg/StateSet>
+#include <osg/StateAttribute>
+#include <osg/PolygonMode>
+#include <osg/LightModel>
+#include <osgDB/WriteFile>
+
+#include "../../kernel/WKernel.h"
+
+#include "../../common/math/WMatrix.h"
+#include "../../common/math/WVector3D.h"
+
+#include "WSphereCreator.h"
+#include "WMGeometryGlyphs.h"
+
+WMGeometryGlyphs::WMGeometryGlyphs():
+    WModule(),
+    m_moduleNode( new WGEGroupNode() )
+{
+}
+
+WMGeometryGlyphs::~WMGeometryGlyphs()
+{
+    // Cleanup!
+    removeConnectors();
+}
+
+boost::shared_ptr< WModule > WMGeometryGlyphs::factory() const
+{
+    // See "src/modules/template/" for an extensively documented example.
+    return boost::shared_ptr< WModule >( new WMGeometryGlyphs() );
+}
+
+const std::string WMGeometryGlyphs::getName() const
+{
+    // Specify your module name here. This name must be UNIQUE!
+    return "GeometryGlyphs";
+}
+
+const std::string WMGeometryGlyphs::getDescription() const
+{
+    // Specify your module description here. Be detailed. This text is read by the user.
+    // See "src/modules/template/" for an extensively documented example.
+    return "Someone should add some documentation here.";
+}
+
+void WMGeometryGlyphs::connectors()
+{
+    // Put the code for your connectors here. See "src/modules/template/" for an extensively documented example.
+//    m_input = boost::shared_ptr< WModuleInputData < WDataSetVector > >(
+//            new WModuleInputData< WDataSetVector >( shared_from_this(), "in", "Dataset" ) );
+
+    m_input = boost::shared_ptr< WModuleInputData< WDataSetSingle > >( new WModuleInputData< WDataSetSingle >( shared_from_this(),
+                    "tensor glpyhes input tensor field", "An input set of 2nd-order tensors on a regular 3d-grid." )
+                );
+
+    addConnector( m_input );
+    // call WModules initialization
+    WModule::connectors();
+}
+
+void WMGeometryGlyphs::properties()
+{
+    m_xPos           = m_properties->addProperty( "X Pos of the slice", "Description.", 80 );
+    m_yPos           = m_properties->addProperty( "Y Pos of the slice", "Description.", 100 );
+    m_zPos           = m_properties->addProperty( "Z Pos of the slice", "Description.", 80 );
+
+    m_xPos->setHidden( true );
+    m_yPos->setHidden( true );
+    m_zPos->setHidden( true );
+
+    m_showonX        = m_properties->addProperty( "Show Sagittal", "Show vectors on sagittal slice.", true );
+    m_showonY        = m_properties->addProperty( "Show Coronal", "Show vectors on coronal slice.", true );
+    m_showonZ        = m_properties->addProperty( "Show Axial", "Show vectors on axial slice.", true );
+
+    m_xPos->setMin( 0 );
+    m_xPos->setMax( 160 );
+    m_yPos->setMin( 0 );
+    m_yPos->setMax( 200 );
+    m_zPos->setMin( 0 );
+    m_zPos->setMax( 160 );
+}
+
+void WMGeometryGlyphs::moduleMain()
+{
+    // use the m_input "data changed" flag
+    m_moduleState.setResetable( true, true );
+    m_moduleState.add( m_input->getDataChangedCondition() );
+
+    // signal ready state
+    ready();
+
+    // now, to watch changing/new textures use WSubject's change condition
+    //boost::signals2::connection con = WDataHandler::getDefaultSubject()->getChangeCondition()->subscribeSignal(
+    //boost::bind( &WMMarchingCubes::notifyTextureChange, this ) );
+
+    // loop until the module container requests the module to quit
+    while ( !m_shutdownFlag() )
+    {
+        // acquire data from the input connector
+        m_dataSet = m_input->getData();
+        if ( !m_dataSet.get() )
+        {
+            // OK, the output has not yet sent data
+            // NOTE: see comment at the end of this while loop for m_moduleState
+            debugLog() << "Waiting for data ...";
+            m_moduleState.wait();
+            continue;
+        }
+
+        // do something here
+        prepareGlyphes();
+        //renderMesh();
+
+        // this waits for m_moduleState to fire. By default, this is only the m_shutdownFlag condition.
+        // NOTE: you can add your own conditions to m_moduleState using m_moduleState.add( ... )
+        m_moduleState.wait();
+    }
+}
+
+void WMGeometryGlyphs::prepareGlyphes()
+{
+    WSphereCreator* sc = new WSphereCreator();
+    boost::shared_ptr< WTriangleMesh2 > triMesh( new WTriangleMesh2( 0, 0 ) );
+
+    debugLog() << "Calculating Glyphes";
+
+//    boost::shared_ptr<WTriangleMesh2> sphere1 = sc->createSphere( 0, 15, 50, 20, 50 );
+//    boost::shared_ptr<WTriangleMesh2> sphere2 = sc->createSphere( 1, 15, 50, 60, 50 );
+//    boost::shared_ptr<WTriangleMesh2> sphere3 = sc->createSphere( 2, 15, 50, 100, 50 );
+//    boost::shared_ptr<WTriangleMesh2> sphere4 = sc->createSphere( 3, 15, 50, 140, 50 );
+//    triMesh->addMesh( sphere1 );
+//    triMesh->addMesh( sphere2 );
+//    triMesh->addMesh( sphere3 );
+//    triMesh->addMesh( sphere4 );
+
+    wmath::WPosition current = WKernel::getRunningKernel()->getSelectionManager()->getCrosshair()->getPosition();
+
+    int xPos = current[0];
+    int yPos = current[1];
+    int zPos = current[2];
+
+    m_xPos->set( xPos );
+    m_yPos->set( yPos );
+    m_zPos->set( zPos );
+
+    boost::shared_ptr< WGridRegular3D > grid = boost::shared_dynamic_cast< WGridRegular3D >( m_dataSet->getGrid() );
+    boost::shared_ptr< WValueSet< float > > vals = boost::shared_dynamic_cast< WValueSet<float> >( m_dataSet->getValueSet() );
+
+    m_xPos->setMax( grid->getNbCoordsX() );
+    m_yPos->setMax( grid->getNbCoordsY() );
+    m_zPos->setMax( grid->getNbCoordsZ() );
+
+
+    int maxX = m_xPos->getMax()->getMax();
+    int maxY = m_yPos->getMax()->getMax();
+    //int maxZ = m_zPos->getMax()->getMax();
+
+    wmath::WMatrix< float > m( 3, 3 );
+
+    boost::shared_ptr<WTriangleMesh2> sphere = sc->createSphere( 1 );
+    if ( m_showonZ->get() )
+    {
+        boost::shared_ptr< WProgress > progress = boost::shared_ptr< WProgress >( new WProgress( "GeometryGlyphs", maxX ) );
+        m_progress->addSubProgress( progress );
+
+        for ( int x = 0; x < maxX; ++x )
+        {
+            ++*progress;
+            for ( int y = 0; y < maxY; ++y )
+            {
+                size_t id = ( x + y * maxX + zPos * maxX * maxY ) * 6;
+
+                m( 0, 0 ) = vals->getScalar( id );
+
+                if ( m( 0, 0 ) > 0.000000001 )
+                {
+                    m( 0, 1 ) = vals->getScalar( id + 1 );
+                    m( 0, 2 ) = vals->getScalar( id + 2 );
+
+                    m( 1, 0 ) = vals->getScalar( id + 1 );
+                    m( 1, 1 ) = vals->getScalar( id + 3 );
+                    m( 1, 2 ) = vals->getScalar( id + 4 );
+
+                    m( 2, 0 ) = vals->getScalar( id + 2 );
+                    m( 2, 1 ) = vals->getScalar( id + 4 );
+                    m( 2, 2 ) = vals->getScalar( id + 5 );
+
+
+                    boost::shared_ptr<WTriangleMesh2> sphere1 = sc->createSphere( 1, 400 );
+                    for ( size_t i = 0; i < sphere1->vertSize(); ++i )
+                    {
+                        osg::Vec3 v = sphere1->getVertex( i );
+
+                        float v0 = v[0];
+                        float v1 = v[1];
+                        float v2 = v[2];
+
+                        v[0] = m( 0, 0 ) * v0 + m( 0, 1 ) * v1 + m( 0, 2 ) * v2;
+                        v[1] = m( 1, 0 ) * v0 + m( 1, 1 ) * v1 + m( 1, 2 ) * v2;
+                        v[2] = m( 2, 0 ) * v0 + m( 2, 1 ) * v1 + m( 2, 2 ) * v2;
+
+                        sphere1->setVertex( i, v );
+                    }
+                    triMesh->addMesh( sphere1, x + .5, y + .5, zPos + .5 );
+                }
+            }
+        }
+        progress->finish();
+    }
+    std::cout << triMesh->vertSize() << ":" << triMesh->triangleSize() << std::endl;
+
+    renderMesh( triMesh );
+    m_triMesh = triMesh;
+}
+
+void WMGeometryGlyphs::renderMesh( boost::shared_ptr< WTriangleMesh2 > mesh )
+{
+    m_moduleNode->remove( m_outputGeode );
+    osg::Geometry* surfaceGeometry = new osg::Geometry();
+    m_outputGeode = osg::ref_ptr< osg::Geode >( new osg::Geode );
+
+    m_outputGeode->setName( "glyphes" );
+
+    surfaceGeometry->setVertexArray( mesh->getVertexArray() );
+
+    // ------------------------------------------------
+    // normals
+    surfaceGeometry->setNormalArray( mesh->getVertexNormalArray() );
+    surfaceGeometry->setNormalBinding( osg::Geometry::BIND_PER_VERTEX );
+
+    // ------------------------------------------------
+    // colors
+    //osg::Vec4Array* colors = new osg::Vec4Array;
+    //colors->push_back( osg::Vec4( .9f, .9f, 0.9f, 1.0f ) );
+    surfaceGeometry->setColorArray( mesh->getVertexColorArray() );
+    surfaceGeometry->setColorBinding( osg::Geometry::BIND_PER_VERTEX );
+
+    osg::DrawElementsUInt* surfaceElement = new osg::DrawElementsUInt( osg::PrimitiveSet::TRIANGLES, 0 );
+
+    std::vector< size_t >tris = mesh->getTriangles();
+    surfaceElement->reserve( tris.size() );
+
+    for( unsigned int vertId = 0; vertId < tris.size(); ++vertId )
+    {
+        surfaceElement->push_back( tris[vertId] );
+    }
+    surfaceGeometry->addPrimitiveSet( surfaceElement );
+    m_outputGeode->addDrawable( surfaceGeometry );
+
+    osg::StateSet* state = m_outputGeode->getOrCreateStateSet();
+    osg::ref_ptr<osg::LightModel> lightModel = new osg::LightModel();
+    lightModel->setTwoSided( true );
+    state->setAttributeAndModes( lightModel.get(), osg::StateAttribute::ON );
+    state->setMode(  GL_BLEND, osg::StateAttribute::ON );
+
+//    {
+//        osg::ref_ptr< osg::Material > material = new osg::Material();
+//        material->setDiffuse(   osg::Material::FRONT, osg::Vec4( 1.0, 1.0, 1.0, 1.0 ) );
+//        material->setSpecular(  osg::Material::FRONT, osg::Vec4( 0.0, 0.0, 0.0, 1.0 ) );
+//        material->setAmbient(   osg::Material::FRONT, osg::Vec4( 0.1, 0.1, 0.1, 1.0 ) );
+//        material->setEmission(  osg::Material::FRONT, osg::Vec4( 0.0, 0.0, 0.0, 1.0 ) );
+//        material->setShininess( osg::Material::FRONT, 25.0 );
+//        state->setAttribute( material );
+//    }
+
+    m_moduleNode->insert( m_outputGeode );
+    WKernel::getRunningKernel()->getGraphicsEngine()->getScene()->insert( m_moduleNode );
+}

src/modules/geometryGlyphs/WMGeometryGlyphs.h

+//---------------------------------------------------------------------------
+//
+// Project: OpenWalnut ( http://www.openwalnut.org )
+//
+// Copyright 2009 OpenWalnut Community, BSV-Leipzig and CNCF-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 WMGEOMETRYGLYPHS_H
+#define WMGEOMETRYGLYPHS_H
+
+#include <string>
+
+#include <osg/Node>
+#include <osg/Geode>
+#include <osg/Uniform>
+
+#include "../../kernel/WModule.h"
+#include "../../kernel/WModuleInputData.h"
+#include "../../kernel/WModuleOutputData.h"
+
+#include "../../dataHandler/WDataSetSingle.h"
+#include "../../dataHandler/WDataSetVector.h"
+
+#include "../../graphicsEngine/WGEGroupNode.h"
+#include "../../graphicsEngine/WTriangleMesh2.h"
+
+/** 
+ * Someone should add some documentation here.
+ * Probably the best person would be the module's
+ * creator, i.e. "schurade".
+ *
+ * This is only an empty template for a new module. For
+ * an example module containing many interesting concepts
+ * and extensive documentation have a look at "src/modules/template"
+ *
+ * \ingroup modules
+ */
+class WMGeometryGlyphs: public WModule
+{
+public:
+
+    /**
+     *
+     */
+    WMGeometryGlyphs();
+
+    /**
+     *
+     */
+    virtual ~WMGeometryGlyphs();
+
+    /**
+     * Gives back the name of this module.
+     * \return the module's name.
+     */
+    virtual const std::string getName() const;
+
+    /**
+     * Gives back a description of this module.
+     * \return description to module.
+     */
+    virtual const std::string getDescription() const;
+
+    /**
+     * Due to the prototype design pattern used to build modules, this method returns a new instance of this method. NOTE: it
+     * should never be initialized or modified in some other way. A simple new instance is required.
+     *
+     * \return the prototype used to create every module in OpenWalnut.
+     */
+    virtual boost::shared_ptr< WModule > factory() const;
+
+protected:
+
+    /**
+     * Entry point after loading the module. Runs in separate thread.
+     */
+    virtual void moduleMain();
+
+    /**
+     * Initialize the connectors this module is using.
+     */
+    virtual void connectors();
+
+    /**
+     * Initialize the properties for this module.
+     */
+    virtual void properties();
+
+
+private:
+    void prepareGlyphes(); //!< initial creation of glyphs
+
+    /**
+     * render function
+     * \param mesh
+     */
+    void renderMesh( boost::shared_ptr< WTriangleMesh2 > mesh );
+
+    WPropBool m_useTextureProp; //!< Property indicating whether to use texturing with scalar data sets.
+
+    osg::ref_ptr< WGEGroupNode > m_moduleNode; //!< Pointer to the modules group node. We need it to be able to update it when callback is invoked.
+
+    osg::ref_ptr< osg::Geode > m_outputGeode; //!< Pointer to geode containing the glpyhs
+
+    boost::shared_ptr< WModuleInputData< WDataSetSingle > > m_input;  //!< Input connector required by this module.
+
+    boost::shared_ptr< const WDataSetSingle > m_dataSet; //!< pointer to dataSet to be able to access it throughout the whole module.
+
+    boost::shared_ptr< WTriangleMesh2 > m_triMesh; //!< This triangle mesh is provided as output through the connector.
+
+    WPropInt      m_xPos; //!< x posistion of the slice
+
+    WPropInt      m_yPos; //!< y posistion of the slice
+
+    WPropInt      m_zPos; //!< z posistion of the slice
+
+    WPropBool     m_showonX; //!< in dicates whether the vector should be shown on slice X
+
+    WPropBool     m_showonY; //!< in dicates whether the vector should be shown on slice Y
+
+    WPropBool     m_showonZ; //!< in dicates whether the vector should be shown on slice Z
+};
+
+#endif  // WMGEOMETRYGLYPHS_H

src/modules/geometryGlyphs/WSphereCreator.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.
+//