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//---------------------------------------------------------------------------
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// Project: OpenWalnut ( http://www.openwalnut.org )
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// Copyright 2009 OpenWalnut Community, BSV-Leipzig and CNCF-CBS
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// For more information see http://www.openwalnut.org/copying
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// This file is part of OpenWalnut.
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// OpenWalnut is free software: you can redistribute it and/or modify
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// it under the terms of the GNU Lesser General Public License as published by
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// the Free Software Foundation, either version 3 of the License, or
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// (at your option) any later version.
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// OpenWalnut is distributed in the hope that it will be useful,
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// but WITHOUT ANY WARRANTY; without even the implied warranty of
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// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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// GNU Lesser General Public License for more details.
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// You should have received a copy of the GNU Lesser General Public License
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// along with OpenWalnut. If not, see <http://www.gnu.org/licenses/>.
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//---------------------------------------------------------------------------
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#include <osg/Geometry>
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#include <osg/StateSet>
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#include <osg/StateAttribute>
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#include <osg/PolygonMode>
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#include <osg/LightModel>
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#include "core/kernel/WKernel.h"
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#include "core/graphicsEngine/WGEUtils.h"
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#include "core/graphicsEngine/shaders/WGEPropertyUniform.h"
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#include "WMSuperquadricGlyphs.h"
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#include "WMSuperquadricGlyphs.xpm"
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// This line is needed by the module loader to actually find your module.
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W_LOADABLE_MODULE( WMSuperquadricGlyphs )
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WMSuperquadricGlyphs::WMSuperquadricGlyphs():
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WMSuperquadricGlyphs::~WMSuperquadricGlyphs()
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boost::shared_ptr< WModule > WMSuperquadricGlyphs::factory() const
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return boost::shared_ptr< WModule >( new WMSuperquadricGlyphs() );
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const char** WMSuperquadricGlyphs::getXPMIcon() const
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return superquadricglyphs_xpm;
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const std::string WMSuperquadricGlyphs::getName() const
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return "Superquadric Glyphs";
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const std::string WMSuperquadricGlyphs::getDescription() const
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return "GPU based ray-tracing of second order, superquadric tensor glyphs.";
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void WMSuperquadricGlyphs::connectors()
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// The input second order tensor dataset
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m_input = boost::shared_ptr< WModuleInputData< WDataSetDTI > >( new WModuleInputData< WDataSetDTI >( shared_from_this(),
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"tensor input", "An input set of 2nd-order tensors on a regular 3D-grid." )
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addConnector( m_input );
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// call WModule's initialization
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WModule::connectors();
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void WMSuperquadricGlyphs::properties()
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// The condition fires on property updates
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m_propCondition = boost::shared_ptr< WCondition >( new WCondition() );
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// The slice positions. These get update externally
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m_xPos = m_properties->addProperty( "Sagittal position", "Slice X position.", 0, m_propCondition );
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m_yPos = m_properties->addProperty( "Coronal position", "Slice Y position.", 0, m_propCondition );
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m_zPos = m_properties->addProperty( "Axial position", "Slice Z position.", 0, m_propCondition );
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// Flags denoting whether the glyphs should be shown on the specific slice
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// NOTE: the showon* properties do not need to notify m_propCondition as they get handled by the slice's osg node.
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m_showonX = m_properties->addProperty( "Show sagittal", "Show vectors on sagittal slice.", true );
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m_showonY = m_properties->addProperty( "Show coronal", "Show vectors on coronal slice.", true );
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m_showonZ = m_properties->addProperty( "Show axial", "Show vectors on axial slice.", true );
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// Thresholding for filtering glyphs
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m_evThreshold = m_properties->addProperty( "Eigenvalue threshold",
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"Clip Glyphs whose smallest eigenvalue is below the given threshold.", 0.01 );
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m_evThreshold->setMin( 0.0 );
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m_evThreshold->setMax( 1.0 );
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m_faThreshold = m_properties->addProperty( "FA threshold",
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"Clip Glyphs whose fractional anisotropy is below the given threshold.", 0.01 );
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m_faThreshold->setMin( 0.0 );
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m_faThreshold->setMax( 1.0 );
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m_gamma = m_properties->addProperty( "Gamma", "Sharpness Parameter of the SuperQuadrics.", 10.0 );
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m_gamma->setMin( 0.0 );
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m_gamma->setMax( 10.0 );
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m_scaling = m_properties->addProperty( "Scaling", "Scaling of Glyphs.", 0.5 );
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m_scaling->setMin( 0.0 );
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m_scaling->setMax( 2.0 );
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inline void WMSuperquadricGlyphs::addGlyph( osg::Vec3 position, osg::ref_ptr< osg::Vec3Array > vertices, osg::ref_ptr< osg::Vec3Array > orientation )
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vertices->push_back( position );
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orientation->push_back( osg::Vec3( -1.0, -1.0, -1.0 ) );
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vertices->push_back( position );
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orientation->push_back( osg::Vec3( 1.0, -1.0, -1.0 ) );
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vertices->push_back( position );
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orientation->push_back( osg::Vec3( 1.0, 1.0, -1.0 ) );
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vertices->push_back( position );
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orientation->push_back( osg::Vec3( -1.0, 1.0, -1.0 ) );
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vertices->push_back( position );
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orientation->push_back( osg::Vec3( -1.0, -1.0, 1.0 ) );
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vertices->push_back( position );
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orientation->push_back( osg::Vec3( 1.0, -1.0, 1.0 ) );
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vertices->push_back( position );
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orientation->push_back( osg::Vec3( 1.0, 1.0, 1.0 ) );
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vertices->push_back( position );
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orientation->push_back( osg::Vec3( -1.0, 1.0, 1.0 ) );
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vertices->push_back( position );
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orientation->push_back( osg::Vec3( -1.0, 1.0, -1.0 ) );
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vertices->push_back( position );
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orientation->push_back( osg::Vec3( 1.0, 1.0, -1.0 ) );
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vertices->push_back( position );
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orientation->push_back( osg::Vec3( 1.0, 1.0, 1.0 ) );
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vertices->push_back( position );
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orientation->push_back( osg::Vec3( -1.0, 1.0, 1.0 ) );
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vertices->push_back( position );
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orientation->push_back( osg::Vec3( -1.0, -1.0, -1.0 ) );
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vertices->push_back( position );
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orientation->push_back( osg::Vec3( 1.0, -1.0, -1.0 ) );
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vertices->push_back( position );
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orientation->push_back( osg::Vec3( 1.0, -1.0, 1.0 ) );
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vertices->push_back( position );
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orientation->push_back( osg::Vec3( -1.0, -1.0, 1.0 ) );
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vertices->push_back( position );
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orientation->push_back( osg::Vec3( -1.0, -1.0, -1.0 ) );
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vertices->push_back( position );
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orientation->push_back( osg::Vec3( -1.0, 1.0, -1.0 ) );
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vertices->push_back( position );
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orientation->push_back( osg::Vec3( -1.0, 1.0, 1.0 ) );
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vertices->push_back( position );
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orientation->push_back( osg::Vec3( -1.0, -1.0, 1.0 ) );
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vertices->push_back( position );
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orientation->push_back( osg::Vec3( 1.0, -1.0, -1.0 ) );
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vertices->push_back( position );
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orientation->push_back( osg::Vec3( 1.0, 1.0, -1.0 ) );
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vertices->push_back( position );
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orientation->push_back( osg::Vec3( 1.0, 1.0, 1.0 ) );
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vertices->push_back( position );
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orientation->push_back( osg::Vec3( 1.0, -1.0, 1.0 ) );
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void WMSuperquadricGlyphs::addTensor( size_t idx, osg::Vec3Array* diag, osg::Vec3Array* offdiag )
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osg::Vec3 d = osg::Vec3( m_dataSetValueSet->getScalarDouble( idx * 6 + 0 ),
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m_dataSetValueSet->getScalarDouble( idx * 6 + 3 ),
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m_dataSetValueSet->getScalarDouble( idx * 6 + 5 ) );
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osg::Vec3 o = osg::Vec3( m_dataSetValueSet->getScalarDouble( idx * 6 + 1 ),
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m_dataSetValueSet->getScalarDouble( idx * 6 + 2 ),
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m_dataSetValueSet->getScalarDouble( idx * 6 + 4 ) );
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// we need to add it for every vertex per glyph!
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for( size_t c = 0; c < 6 * 4; ++c )
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diag->push_back( d );
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offdiag->push_back( o );
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void WMSuperquadricGlyphs::initOSG()
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// The Idea behind all this is to have fast updates when the navigation slices move. By presetting glyph vertex and tex coords -> fast change
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// of diag and offdiag tex arrays possible. The slices are moved using the transform nodes
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debugLog() << "Grid Size: " << m_maxX << "x" << m_maxY << "x" << m_maxZ;
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debugLog() << "Creating " << m_nbGlyphsX + m_nbGlyphsY + m_nbGlyphsZ << " glyphs.";
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// remove the old slices
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m_output->remove( m_xSlice );
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m_output->remove( m_ySlice );
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m_output->remove( m_zSlice );
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// create all the transformation nodes
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m_xSlice = new WGEManagedGroupNode( m_showonX );
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m_xSlice->setMatrix( osg::Matrixd::identity() );
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m_ySlice = new WGEManagedGroupNode( m_showonY );
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m_ySlice->setMatrix( osg::Matrixd::identity() );
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m_zSlice = new WGEManagedGroupNode( m_showonZ );
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m_zSlice->setMatrix( osg::Matrixd::identity() );
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// init the vertex arrays
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osg::ref_ptr< osg::Geode > geode;
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osg::ref_ptr< osg::Geometry > geometry;
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osg::ref_ptr< osg::DrawArrays > da;
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// NOTE: it would be nice to use one vertex and tex array for all the three but this disallows us to replace the tensor diag/offdiag arrays
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// for each slide separately.
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osg::ref_ptr< osg::Vec3Array > vertices;
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osg::ref_ptr< osg::Vec3Array > texcoords0;
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// fill the geode with glyph proxy geometry for a slice
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vertices = new osg::Vec3Array;
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vertices->reserve( m_nbGlyphsX * 6 * 4 );
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texcoords0 = new osg::Vec3Array;
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texcoords0->reserve( m_nbGlyphsX * 6 * 4 );
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geometry = new osg::Geometry();
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geometry->setDataVariance( osg::Object::DYNAMIC );
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geometry->setVertexArray( vertices );
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geometry->setUseVertexBufferObjects( true );
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geometry->setTexCoordArray( 0, texcoords0 );
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da = new osg::DrawArrays( osg::PrimitiveSet::QUADS, 0, m_nbGlyphsX * 6 * 4 );
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geometry->addPrimitiveSet( da );
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// create a new geode containing the glyphs proxy geometry
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geode = new osg::Geode();
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geode->addDrawable( geometry );
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// add a glyph at every position
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for( size_t z = 0; z < m_maxZ; ++z )
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for( size_t y = 0; y < m_maxY; ++y )
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addGlyph( osg::Vec3d( 0.0, y, z ), vertices, texcoords0 );
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// set some callbacks
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m_xSliceGlyphCallback = new GlyphGeometryNodeCallback( geometry );
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geometry->setUpdateCallback( m_xSliceGlyphCallback );
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m_xSlice->addUpdateCallback( new WGELinearTranslationCallback< WPropInt >( osg::Vec3( 1.0, 0.0, 0.0 ), m_xPos ) );
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m_xSlice->addChild( geode );
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// Y Slice, sorry for code duplication.
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// fill the geode with glyph proxy geometry for a slice
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vertices = new osg::Vec3Array;
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vertices->reserve( m_nbGlyphsX * 6 * 4 );
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texcoords0 = new osg::Vec3Array;
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texcoords0->reserve( m_nbGlyphsX * 6 * 4 );
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geometry = new osg::Geometry();
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geometry->setDataVariance( osg::Object::DYNAMIC );
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geometry->setVertexArray( vertices );
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geometry->setUseVertexBufferObjects( true );
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geometry->setTexCoordArray( 0, texcoords0 );
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da = new osg::DrawArrays( osg::PrimitiveSet::QUADS, 0, m_nbGlyphsY * 6 * 4 );
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geometry->addPrimitiveSet( da );
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// create a new geode containing the glyphs proxy geometry
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geode = new osg::Geode();
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geode->addDrawable( geometry );
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// add a glyph at every position
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for( size_t z = 0; z < m_maxZ; ++z )
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for( size_t x = 0; x < m_maxX; ++x )
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addGlyph( osg::Vec3d( x, 0.0, z ), vertices, texcoords0 );
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// set some callbacks
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m_ySliceGlyphCallback = new GlyphGeometryNodeCallback( geometry );
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geometry->setUpdateCallback( m_ySliceGlyphCallback );
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m_ySlice->addUpdateCallback( new WGELinearTranslationCallback< WPropInt >( osg::Vec3( 0.0, 1.0, 0.0 ), m_yPos ) );
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m_ySlice->addChild( geode );
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// Z Slice, sorry for code duplication.
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// fill the geode with glyph proxy geometry for a slice
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vertices = new osg::Vec3Array;
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vertices->reserve( m_nbGlyphsX * 6 * 4 );
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texcoords0 = new osg::Vec3Array;
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texcoords0->reserve( m_nbGlyphsX * 6 * 4 );
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geometry = new osg::Geometry();
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geometry->setDataVariance( osg::Object::DYNAMIC );
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geometry->setVertexArray( vertices );
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geometry->setUseVertexBufferObjects( true );
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geometry->setTexCoordArray( 0, texcoords0 );
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da = new osg::DrawArrays( osg::PrimitiveSet::QUADS, 0, m_nbGlyphsZ * 6 * 4 );
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geometry->addPrimitiveSet( da );
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// create a new geode containing the glyphs proxy geometry
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geode = new osg::Geode();
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geode->addDrawable( geometry );
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// add a glyph at every position
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for( size_t y = 0; y < m_maxY; ++y )
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for( size_t x = 0; x < m_maxX; ++x )
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addGlyph( osg::Vec3d( x, y, 0.0 ), vertices, texcoords0 );
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// set some callbacks
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m_zSliceGlyphCallback = new GlyphGeometryNodeCallback( geometry );
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geometry->setUpdateCallback( m_zSliceGlyphCallback );
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m_zSlice->addUpdateCallback( new WGELinearTranslationCallback< WPropInt >( osg::Vec3( 0.0, 0.0, 1.0 ), m_zPos ) );
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m_zSlice->addChild( geode );
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// add the transformation nodes to the output group
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m_output->insert( m_xSlice );
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m_output->insert( m_ySlice );
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m_output->insert( m_zSlice );
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void WMSuperquadricGlyphs::GlyphGeometryNodeCallback::update( osg::NodeVisitor* /*nv*/, osg::Drawable* /*d*/ )
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// update the tex array
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m_geometry->setTexCoordArray( 1, m_tensorDiag );
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m_geometry->setTexCoordArray( 2, m_tensorOffDiag );
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void WMSuperquadricGlyphs::GlyphGeometryNodeCallback::setNewTensorData( osg::ref_ptr< osg::Vec3Array > diag, osg::ref_ptr< osg::Vec3Array > offdiag )
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m_tensorOffDiag = offdiag;
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void WMSuperquadricGlyphs::moduleMain()
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// use the m_input "data changed" flag
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m_moduleState.setResetable( true, true );
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m_moduleState.add( m_input->getDataChangedCondition() );
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// use property condition to wake up on property changes
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m_moduleState.add( m_propCondition );
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// signal ready state
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// create all these geodes we need
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m_output = osg::ref_ptr< WGEManagedGroupNode > ( new WGEManagedGroupNode( m_active ) );
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WKernel::getRunningKernel()->getGraphicsEngine()->getScene()->insert( m_output );
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osg::ref_ptr< osg::StateSet > sset = m_output->getOrCreateStateSet();
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sset->setMode( GL_LIGHTING, osg::StateAttribute::OFF );
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m_shader = osg::ref_ptr< WGEShader > ( new WGEShader( "WMSuperquadricGlyphs", m_localPath ) );
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m_shader->apply( m_output );
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// set uniform callbacks and uniforms
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osg::ref_ptr< osg::Uniform > evThreshold = new WGEPropertyUniform< WPropDouble >( "u_evThreshold", m_evThreshold );
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osg::ref_ptr< osg::Uniform > faThreshold = new WGEPropertyUniform< WPropDouble >( "u_faThreshold", m_faThreshold );
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osg::ref_ptr< osg::Uniform > scaling = new WGEPropertyUniform< WPropDouble >( "u_scaling", m_scaling );
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osg::ref_ptr< osg::Uniform > gamma = new WGEPropertyUniform< WPropDouble >( "u_gamma", m_gamma );
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sset->addUniform( evThreshold );
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sset->addUniform( faThreshold );
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sset->addUniform( scaling );
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sset->addUniform( gamma );
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bool initialTensorUpload = true;
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// loop until the module container requests the module to quit
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while( !m_shutdownFlag() )
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m_moduleState.wait();
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////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
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// After waking up, the module has to check whether the shutdownFlag fired. If yes, simply quit the module.
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// woke up since the module is requested to finish
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if( m_shutdownFlag() )
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////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
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// has the data changes? And even more important: is it valid?
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boost::shared_ptr< WDataSetDTI > newDataSet = m_input->getData();
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bool dataChanged = ( m_dataSet != newDataSet );
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bool dataValid = ( newDataSet );
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// if data is invalid, remove rendering
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debugLog() << "Resetting.";
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////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
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if( dataChanged && dataValid )
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// The data is different. Copy it to our internal data variable:
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debugLog() << "Received Data.";
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initialTensorUpload = true;
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// also provide progress information
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boost::shared_ptr< WProgress > progress1 = boost::shared_ptr< WProgress >( new WProgress( "Building Glyph Geometry" ) );
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m_progress->addSubProgress( progress1 );
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// get pointers for the new data
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m_dataSet = newDataSet;
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m_dataSetGrid = boost::shared_dynamic_cast< WGridRegular3D >( m_dataSet->getGrid() );
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WAssert( m_dataSetGrid, "Dataset does not have a regular 3D grid." );
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m_maxX = m_dataSetGrid->getNbCoordsX();
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m_maxY = m_dataSetGrid->getNbCoordsY();
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m_maxZ = m_dataSetGrid->getNbCoordsZ();
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m_dataSetValueSet = m_dataSet->getValueSet();
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m_nbGlyphsX = m_maxY * m_maxZ;
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m_nbGlyphsY = m_maxX * m_maxZ;
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m_nbGlyphsZ = m_maxX * m_maxY;
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m_xPos->setMax( m_maxX );
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m_xPos->set( m_maxX / 2 );
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m_yPos->setMax( m_maxY );
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m_yPos->set( m_maxY / 2 );
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m_zPos->setMax( m_maxZ );
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m_zPos->set( m_maxZ / 2 );
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m_output->setMatrix( static_cast< WMatrix4d >( m_dataSetGrid->getTransform() ) );
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// new data -> update OSG Stuff
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if( dataValid && ( m_xPos->changed() || initialTensorUpload ) )
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// also provide progress information
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boost::shared_ptr< WProgress > progress1 = boost::shared_ptr< WProgress >( new WProgress( "Building Glyph Geometry" ) );
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m_progress->addSubProgress( progress1 );
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osg::ref_ptr< osg::Vec3Array > diag = new osg::Vec3Array;
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diag->reserve( m_nbGlyphsX * 6 * 4 );
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osg::ref_ptr< osg::Vec3Array > offdiag = new osg::Vec3Array;
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offdiag->reserve( m_nbGlyphsX * 6 * 4 );
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// this updates the diag/offdiag texture coordinate arrays of the xSlice
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// x = const -> handle xPos property
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size_t fixedX = m_xPos->get( true );
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for( size_t z = 0; z < m_maxZ; ++z )
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// Calculate the current position along the z direction
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size_t zPre = fixedX + z * m_maxX * m_maxY;
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for( size_t y = 0; y < m_maxY; ++y )
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addTensor( zPre + y * m_maxX, diag, offdiag );
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m_xSliceGlyphCallback->setNewTensorData( diag, offdiag );
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if( dataValid && ( m_yPos->changed() || initialTensorUpload ) )
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// also provide progress information
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boost::shared_ptr< WProgress > progress1 = boost::shared_ptr< WProgress >( new WProgress( "Building Glyph Geometry" ) );
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m_progress->addSubProgress( progress1 );
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osg::ref_ptr< osg::Vec3Array > diag = new osg::Vec3Array;
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diag->reserve( m_nbGlyphsX * 6 * 4 );
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osg::ref_ptr< osg::Vec3Array > offdiag = new osg::Vec3Array;
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offdiag->reserve( m_nbGlyphsX * 6 * 4 );
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// y = const -> handle yPos property
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size_t fixedY = m_yPos->get( true );
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size_t fixedYOffset = fixedY * m_maxX;
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for( size_t z = 0; z < m_maxZ; ++z )
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// Calculate current offset for value index
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size_t zPre = fixedYOffset + ( z * m_maxX * m_maxY );
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for( size_t x = 0; x < m_maxX; ++x )
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addTensor( zPre + x, diag, offdiag );
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m_ySliceGlyphCallback->setNewTensorData( diag, offdiag );
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if( dataValid && ( m_zPos->changed() || initialTensorUpload ) )
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// also provide progress information
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boost::shared_ptr< WProgress > progress1 = boost::shared_ptr< WProgress >( new WProgress( "Building Glyph Geometry" ) );
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m_progress->addSubProgress( progress1 );
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osg::ref_ptr< osg::Vec3Array > diag = new osg::Vec3Array;
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diag->reserve( m_nbGlyphsX * 6 * 4 );
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osg::ref_ptr< osg::Vec3Array > offdiag = new osg::Vec3Array;
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offdiag->reserve( m_nbGlyphsX * 6 * 4 );
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// z = const -> handle zPos property
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size_t fixedZ = static_cast< size_t >( m_zPos->get( true ) );
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size_t fixedZOffset = fixedZ * m_maxX * m_maxY;
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for( size_t y = 0; y < m_maxY; ++y )
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// Calculate current offset for value index
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size_t yPre = fixedZOffset + ( y * m_maxX );
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for( size_t x = 0; x < m_maxX; ++x )
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addTensor( yPre + x, diag, offdiag );
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m_zSliceGlyphCallback->setNewTensorData( diag, offdiag );
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initialTensorUpload = false;
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// At this point, the container managing this module signalled to shutdown. The main loop has ended and you should clean up. Always remove
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// allocated memory and remove all OSG nodes.
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WKernel::getRunningKernel()->getGraphicsEngine()->getScene()->remove( m_output );
added
removed
src/modules/superquadricGlyphs/WMSuperquadricGlyphs.cpp
