[ADD] adding image space tensor LIC algorithm. Complete and working implementation.

src/modules/imageSpaceTensorLIC/WMImageSpaceTensorLIC.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 WMIMAGESPACETENSORLIC_H
+#define WMIMAGESPACETENSORLIC_H
+
+#include <string>
+#include <vector>
+
+#include "core/dataHandler/WDataSetVector.h"
+
+#include "core/graphicsEngine/WTriangleMesh.h"
+#include "core/graphicsEngine/WGEManagedGroupNode.h"
+
+#include "core/kernel/WModule.h"
+#include "core/kernel/WModuleInputData.h"
+
+/**
+ * This module takes a second order symmetric tensor dataset and uses it to apply an image space based (fast) fabric-like LIC to an arbitrary
+ * surface. The surface can be specified as tri mesh or, if not specified, slices.
+ *
+ * \ingroup modules
+ */
+class WMImageSpaceTensorLIC: public WModule
+{
+public:
+    /**
+     * Default constructor.
+     */
+    WMImageSpaceTensorLIC();
+
+    /**
+     * Destructor.
+     */
+    virtual ~WMImageSpaceTensorLIC();
+
+    /**
+     * 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:
+    /**
+     * Initializes the needed geodes, transformations and vertex arrays. This needs to be done once for each new dataset.
+     *
+     * \param grid the grid to places the slices in
+     * \param mesh the mesh to use if not NULL and m_useSlices is false
+     */
+    void initOSG( boost::shared_ptr< WGridRegular3D > grid, boost::shared_ptr< WTriangleMesh > mesh );
+
+    /**
+     * The input connector containing the DTI field whose derived field is used for LIC.
+     */
+    boost::shared_ptr< WModuleInputData< WDataSetVector > > m_evec1In;
+
+    /**
+     * The input connector containing the DTI field whose derived field is used for LIC.
+     */
+    boost::shared_ptr< WModuleInputData< WDataSetVector > > m_evec2In;
+
+    /**
+     * The input connector containing the DTI field whose derived field is used for LIC.
+     */
+    boost::shared_ptr< WModuleInputData< WDataSetVector > > m_evalsIn;
+
+    /**
+     * The input containing the surface on which the LIC should be applied on
+     */
+    boost::shared_ptr< WModuleInputData< WTriangleMesh > > m_meshIn;
+
+    /**
+     * A property allowing the user to select whether the slices or the mesh should be used
+     */
+    WPropSelection m_geometrySelection;
+
+    /**
+     * A list of items that can be selected using m_geometrySelection.
+     */
+    boost::shared_ptr< WItemSelection > m_geometrySelections;
+
+    /**
+     * A condition used to notify about changes in several properties.
+     */
+    boost::shared_ptr< WCondition > m_propCondition;
+
+    /**
+     * The Geode containing all the slices and the mesh
+     */
+    osg::ref_ptr< WGEGroupNode > m_output;
+
+    /**
+     * Scene root node.
+     */
+    osg::ref_ptr< WGEManagedGroupNode > m_root;
+
+    WPropGroup    m_sliceGroup; //!< the group contains several slice properties
+
+    WPropGroup    m_geometryGroup; //!< the group contains several input geometry parameters
+
+    WPropGroup    m_licGroup; //!< the group contains several LIC properties
+
+    WPropBool     m_useSlices; //!< indicates whether the vector should be shown on slices or input geometry
+
+    WPropInt      m_xPos; //!< x position of the slice
+
+    WPropInt      m_yPos; //!< y position of the slice
+
+    WPropInt      m_zPos; //!< z position of the slice
+
+    WPropBool     m_showonX; //!< indicates whether the vector should be shown on slice X
+
+    WPropBool     m_showonY; //!< indicates whether the vector should be shown on slice Y
+
+    WPropBool     m_showonZ; //!< indicates whether the vector should be shown on slice Z
+
+    WPropBool     m_showHUD; //!< indicates whether to show the texture HUD
+
+    WPropBool     m_useEdges; //!< indicates whether to show the edges
+
+    WPropColor    m_useEdgesColor; //!< indicated whether the edges (if enabled) should be black or white or green or red or ....
+
+    WPropDouble   m_useEdgesStep; //!< define the steepness of the step function used to blend in the edge color.
+
+    WPropBool     m_useLight; //!< indicates whether to use Phong
+
+    WPropDouble   m_lightIntensity; //!< light intensity
+
+    WPropInt      m_numIters; //!< the number of iterations done per frame
+
+    WPropDouble   m_cmapRatio; //!< the ratio between colormap and LIC
+
+    WPropDouble   m_projectionAngleThreshold; //!< the angle threshold between surface and vector before clipping the vector.
+
+    /**
+     * The group for more advanced LIC features
+     */
+    WPropGroup    m_advancedLicGroup;
+
+    /**
+     * The resolution scaling for the noise
+     */
+    WPropDouble   m_noiseRes;
+
+    /**
+     * Clipp according to FA.
+     */
+    WPropDouble   m_faClip;
+};
+
+#endif  // WMIMAGESPACETENSORLIC_H
+

src/modules/imageSpaceTensorLIC/WToolkit.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/>.
+//
+//---------------------------------------------------------------------------
+
+// This file's purpose is to provide a list of modules and additional extensions as entry point for OpenWalnut's module loader.
+// Both functAdd your modules here. If you miss this step, OpenWalnut will not be able to load your modules/extensions.
+
+#include <boost/shared_ptr.hpp>
+
+#include <core/kernel/WModule.h>
+
+#include "WMImageSpaceTensorLIC.h"
+
+/**
+ * This function is called by OpenWalnut, when loading your library to learn about the modules you provide. The function is called with a given
+ * list reference, where you add all of your modules. Modules which are not registered this way, cannot be used in OpenWalnut. As this is called
+ * before loading any project file or running any module, it is ensured that you can rely on the modules provided here in your project files and
+ * other modules.
+ *
+ * \note this function is optional. You can remove it if you do not need it.
+ *
+ * \param m the list of modules. Add you module instances into this list.
+ */
+extern "C" void WLoadModule( WModuleList& m ) // NOLINT
+{
+    // This line is needed by the module loader to actually find your module. You need to add this to your module too. Do NOT add a ";" here.
+    m.push_back( boost::shared_ptr< WModule >( new WMImageSpaceTensorLIC ) );
+}
+

src/modules/imageSpaceTensorLIC/WTuringTextureCreator.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 <iostream>
+#include <vector>
+
+#include <boost/random.hpp>
+
+#include <core/common/exceptions/WPreconditionNotMet.h>
+
+#include "WTuringTextureCreator.h"
+
+WTuringTextureCreator::WTuringTextureCreator( std::size_t numThreads )
+    : m_numIterations( 100 ),
+      m_spotIrregularity( 0.1 ),
+      m_spotSize( 0.1 )
+{
+    WPrecond( numThreads > 0, "" );
+
+    for( std::size_t k = 0; k < numThreads; ++k )
+    {
+        m_threads.push_back( boost::shared_ptr< TextureThread >( new TextureThread( k, numThreads ) ) );
+    }
+}
+
+WTuringTextureCreator::~WTuringTextureCreator()
+{
+}
+
+void WTuringTextureCreator::setNumIterations( std::size_t iter )
+{
+    WPrecond( iter > 0, "Invalid number of iterations!" );
+
+    m_numIterations = iter;
+}
+
+void WTuringTextureCreator::setSpotIrregularity( float irr )
+{
+    WPrecond( irr >= 0.0f && irr <= 1.0f, "Spot irregularity must be in [0,1]!" );
+
+    m_spotIrregularity = irr;
+}
+
+void WTuringTextureCreator::setSpotSize( float size )
+{
+    WPrecond( size >= 0.0f && size <= 1.0f, "Spot size must be in [0,1]!" );
+
+    m_spotSize = size;
+}
+
+osg::ref_ptr< WGETexture3D > WTuringTextureCreator::create( std::size_t sizeX, std::size_t sizeY, std::size_t sizeZ )
+{
+    // some constants, maybe change to parameters
+    float const spotFactor = ( 0.02f + 0.58f * ( 1.0f - m_spotSize ) ) / 15.0f;
+    float const d1 = 0.125f;
+    float const d2 = 0.03125f;
+    float const speed = 1.0f;
+
+    std::vector< float > concentration1( sizeX * sizeY * sizeZ, 4.0f );
+    std::vector< float > concentration2( sizeX * sizeY * sizeZ, 4.0f );
+    std::vector< float > delta1( sizeX * sizeY * sizeZ, 0.0f );
+    std::vector< float > delta2( sizeX * sizeY * sizeZ, 0.0f );
+    std::vector< float > noise( sizeX * sizeY * sizeZ );
+
+    boost::mt19937 generator( std::time( 0 ) );
+
+    float noiseRange = 0.1f + 4.9f * m_spotIrregularity;
+
+    boost::uniform_real< float > dist( 12.0f - noiseRange, 12.0f + noiseRange );
+    boost::variate_generator< boost::mt19937&, boost::uniform_real< float > > rand( generator, dist );
+
+    // initialize noise
+    for( std::size_t k = 0; k < sizeX * sizeY * sizeZ; ++k )
+    {
+        noise[ k ] = rand();
+    }
+
+    // iterate
+    for( std::size_t iter = 0; iter < m_numIterations; ++iter )
+    {
+        std::cout << "iteration: " << iter << std::endl;
+
+        // step one: calculate change in concentration across the volume
+        for( std::size_t k = 0; k < m_threads.size(); ++k )
+        {
+            m_threads[ k ]->setTextureSize( sizeX, sizeY, sizeZ );
+            m_threads[ k ]->setSpotFactor( spotFactor );
+            m_threads[ k ]->setDiffusionConstants( d1, d2 );
+            m_threads[ k ]->setBufferPointers( &concentration1, &concentration2, &noise, &delta1, &delta2 );
+            m_threads[ k ]->run();
+        }
+
+        for( std::size_t k = 0; k < m_threads.size(); ++k )
+        {
+            m_threads[ k ]->wait();
+        }
+
+        // applying the change in concentration is not too costly
+        for( std::size_t k = 0; k < sizeX * sizeY * sizeZ; ++k )
+        {
+            concentration1[ k ] += speed * delta1[ k ];
+            concentration2[ k ] += speed * delta2[ k ];
+        }
+    }
+
+    // allocate new osg::Image for the texture data
+    osg::ref_ptr< osg::Image > img = new osg::Image;
+    img->allocateImage( sizeX, sizeY, sizeZ, GL_LUMINANCE, GL_UNSIGNED_BYTE );
+
+    // find min and max
+    float c1min = *std::min_element( concentration1.begin(), concentration1.end() );
+    float c1max = *std::max_element( concentration1.begin(), concentration1.end() );
+
+    // copy to image
+    for( std::size_t k = 0; k < sizeX * sizeY * sizeZ; ++k )
+    {
+        img->data()[ k ] = 255.0f * ( concentration1[ k ] - c1min ) / ( c1max - c1min );
+    }
+
+    return osg::ref_ptr< WGETexture< osg::Texture3D > >( new WGETexture< osg::Texture3D >( img ) );
+}
+
+WTuringTextureCreator::TextureThread::TextureThread( std::size_t id, std::size_t max )
+    : WThreadedRunner(),
+      m_id( id ),
+      m_maxThreads( max ),
+      m_sizeX( 2 ),
+      m_sizeY( 2 ),
+      m_sizeZ( 2 ),
+      m_spotFactor( 0.5 ),
+      m_diffusionConstant1( 0.5 ),
+      m_diffusionConstant2( 0.5 )
+{
+}
+
+WTuringTextureCreator::TextureThread::~TextureThread()
+{
+}
+
+void WTuringTextureCreator::TextureThread::setDiffusionConstants( float d1, float d2 )
+{
+    WPrecond( d1 >= 0.0 && d1 <= 1.0, "" );
+    WPrecond( d2 >= 0.0 && d2 <= 1.0, "" );
+
+    m_diffusionConstant1 = d1;
+    m_diffusionConstant2 = d2;
+}
+
+void WTuringTextureCreator::TextureThread::setSpotFactor( float spotFactor )
+{
+    WPrecond( spotFactor > 0.0, "" );
+
+    m_spotFactor = spotFactor;
+}
+
+void WTuringTextureCreator::TextureThread::setTextureSize( std::size_t sizeX, std::size_t sizeY, std::size_t sizeZ )
+{
+    WPrecond( sizeX > 0, "" );
+    WPrecond( sizeY > 0, "" );
+    WPrecond( sizeZ > 0, "" );
+
+    m_sizeX = sizeX;
+    m_sizeY = sizeY;
+    m_sizeZ = sizeZ;
+}
+
+void WTuringTextureCreator::TextureThread::threadMain()
+{
+    WPrecond( m_concentration1 != 0, "Invalid pointer!" );
+    WPrecond( m_concentration2 != 0, "Invalid pointer!" );
+    WPrecond( m_noise != 0, "Invalid pointer!" );
+    WPrecond( m_delta1 != 0, "Invalid pointer!" );
+    WPrecond( m_delta2 != 0, "Invalid pointer!" );
+
+    std::size_t const numVoxels = m_sizeX * m_sizeY * m_sizeZ;
+
+    std::size_t start = m_id * ( numVoxels / m_maxThreads );
+    std::size_t end = ( m_id + 1 ) * ( numVoxels / m_maxThreads );
+
+    if( m_id == m_maxThreads - 1 )
+    {
+        end = numVoxels;
+    }
+
+    for( std::size_t idx = start; idx < end; ++idx )
+    {
+        std::size_t i = idx % m_sizeX;
+        std::size_t j = ( idx / m_sizeX ) % m_sizeY;
+        std::size_t k = ( idx / m_sizeX ) / m_sizeY;
+
+        std::size_t iNext = ( i + 1 ) % m_sizeX;
+        std::size_t iPrev = ( i + m_sizeX - 1 ) % m_sizeX;
+
+        std::size_t jNext = ( j + 1 ) % m_sizeY;
+        std::size_t jPrev = ( j + m_sizeY - 1 ) % m_sizeY;
+
+        std::size_t kNext = ( k + 1 ) % m_sizeZ;
+        std::size_t kPrev = ( k + m_sizeZ - 1 ) % m_sizeZ;
+
+        // estimate change in concentrations using 3d laplace filter
+        float dc1 = 0.0;
+        dc1 += ( *m_concentration1 )[ iPrev + j * m_sizeX + k * m_sizeX * m_sizeY ];
+        dc1 += ( *m_concentration1 )[ iNext + j * m_sizeX + k * m_sizeX * m_sizeY ];
+        dc1 += ( *m_concentration1 )[ i + jPrev * m_sizeX + k * m_sizeX * m_sizeY ];
+        dc1 += ( *m_concentration1 )[ i + jNext * m_sizeX + k * m_sizeX * m_sizeY ];
+        dc1 += ( *m_concentration1 )[ i + j * m_sizeX + kPrev * m_sizeX * m_sizeY ];
+        dc1 += ( *m_concentration1 )[ i + j * m_sizeX + kNext * m_sizeX * m_sizeY ];
+        dc1 -= 6.0f * ( *m_concentration1 )[ idx ];
+
+        float dc2 = 0.0;
+        dc2 += ( *m_concentration2 )[ iPrev + j * m_sizeX + k * m_sizeX * m_sizeY ];
+        dc2 += ( *m_concentration2 )[ iNext + j * m_sizeX + k * m_sizeX * m_sizeY ];
+        dc2 += ( *m_concentration2 )[ i + jPrev * m_sizeX + k * m_sizeX * m_sizeY ];
+        dc2 += ( *m_concentration2 )[ i + jNext * m_sizeX + k * m_sizeX * m_sizeY ];
+        dc2 += ( *m_concentration2 )[ i + j * m_sizeX + kPrev * m_sizeX * m_sizeY ];
+        dc2 += ( *m_concentration2 )[ i + j * m_sizeX + kNext * m_sizeX * m_sizeY ];
+        dc2 -= 6.0f * ( *m_concentration2 )[ idx ];
+
+        // diffusion
+        ( *m_delta1 )[ idx ] = m_spotFactor * ( 16.0f - ( *m_concentration1 )[ idx ] * ( *m_concentration2 )[ idx ] ) + m_diffusionConstant1 * dc1;
+        ( *m_delta2 )[ idx ] = m_spotFactor * ( ( *m_concentration1 )[ idx ] * ( *m_concentration2 )[ idx ] - ( *m_concentration2 )[ idx ] - ( *m_noise )[ idx ] ) + m_diffusionConstant2 * dc2;
+    }
+}
+
+void WTuringTextureCreator::TextureThread::setBufferPointers( std::vector< float > const* concentration1, std::vector< float > const* concentration2,
+                                                              std::vector< float > const* noise, std::vector< float >* delta1, std::vector< float >* delta2 )
+{
+    WPrecond( concentration1 != 0, "Invalid pointer!" );
+    WPrecond( concentration2 != 0, "Invalid pointer!" );
+    WPrecond( noise != 0, "Invalid pointer!" );
+    WPrecond( delta1 != 0, "Invalid pointer!" );
+    WPrecond( delta2 != 0, "Invalid pointer!" );
+
+    m_concentration1 = concentration1;
+    m_concentration2 = concentration2;
+    m_noise = noise;
+    m_delta1 = delta1;
+    m_delta2 = delta2;
+}

src/modules/imageSpaceTensorLIC/WTuringTextureCreator.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 WTURINGTEXTURECREATOR_H
+#define WTURINGTEXTURECREATOR_H
+
+#include <vector>
+
+#include <boost/thread.hpp>
+
+#include <core/common/WThreadedRunner.h>
+#include <core/graphicsEngine/WGETexture.h>
+
+class WTuringTextureCreator
+{
+public:
+
+    WTuringTextureCreator( std::size_t numThreads = boost::thread::hardware_concurrency() );
+
+    ~WTuringTextureCreator();
+
+    osg::ref_ptr< WGETexture3D > create( std::size_t sizeX, std::size_t sizeY, std::size_t sizeZ );
+
+    void setSpotSize( float size );
+
+    void setSpotIrregularity( float irr );
+
+    void setNumIterations( std::size_t iter );
+
+private:
+
+    class TextureThread : public WThreadedRunner
+    {
+    public:
+
+        TextureThread( std::size_t id, std::size_t max );
+
+        ~TextureThread();
+
+        void setTextureSize( std::size_t sizeX, std::size_t sizeY, std::size_t sizeZ );
+
+        void setSpotFactor( float spotFactor );
+
+        void setDiffusionConstants( float d1, float d2 );
+
+        void setBufferPointers( std::vector< float > const* concentration1, std::vector< float > const* concentration2,
+                                std::vector< float > const* noise, std::vector< float >* delta1, std::vector< float >* delta2 );
+
+        virtual void threadMain();
+
+    private: