[MERGE]

src/dataHandler/WDataSet.cpp

@@ -119,3 +119,7 @@ boost::shared_ptr< WProperties > WDataSet::getInformationProperties() const
     return m_infoProperties;
 }
 
+boost::shared_ptr< WDataSet > WDataSet::clone( boost::shared_ptr< WValueSetBase >, boost::shared_ptr< WGrid > ) const
+{
+    return boost::shared_ptr< WDataSet >();
+}

src/dataHandler/WDataSet.h

@@ -149,6 +149,15 @@ public:
      */
     boost::shared_ptr< WProperties > getInformationProperties() const;
 
+    /**
+     * Returns a new dataset with the given valueset and grid that is of the same type as this dataset.
+     *
+     * \param vs The valueset.
+     * \param grid The grid.
+     * \return The new dataset.
+     */
+    virtual boost::shared_ptr< WDataSet > clone( boost::shared_ptr< WValueSetBase > vs, boost::shared_ptr< WGrid > grid ) const;
+
 protected:
 
     /**

src/dataHandler/WDataSetDTI.cpp

@@ -63,3 +63,9 @@ wmath::WTensorSym< 2, 3, float > WDataSetDTI::getTensor( size_t index ) const
     WAssert( values, "The value set of a WDataSetDTI must be a WValueSet< float >, nothing else!" );
     return wmath::WTensorSym< 2, 3, float >( values->getWValue( index ) );
 }
+
+boost::shared_ptr< WDataSet > WDataSetDTI::clone( boost::shared_ptr< WValueSetBase > vs, boost::shared_ptr< WGrid > grid ) const
+{
+    return boost::shared_ptr< WDataSet >( new WDataSetDTI( vs, grid ) );
+}
+

src/dataHandler/WDataSetDTI.h

@@ -89,6 +89,15 @@ public:
      */
     wmath::WTensorSym< 2, 3, float > getTensor( size_t index ) const;
 
+    /**
+     * Returns a new dataset with the given valueset and grid that is of the same type as this dataset.
+     *
+     * \param vs The valueset.
+     * \param grid The grid.
+     * \return The new dataset.
+     */
+    virtual boost::shared_ptr< WDataSet > clone( boost::shared_ptr< WValueSetBase > vs, boost::shared_ptr< WGrid > grid ) const;
+
 protected:
     /**
      * The prototype as singleton.

src/dataHandler/WDataSetScalar.cpp

@@ -167,3 +167,7 @@ boost::shared_ptr< const WValueSetHistogram > WDataSetScalar::getHistogram( size
     return m_histograms[ buckets ];
 }
 
+boost::shared_ptr< WDataSet > WDataSetScalar::clone( boost::shared_ptr< WValueSetBase > vs, boost::shared_ptr< WGrid > grid ) const
+{
+    return boost::shared_ptr< WDataSet >( new WDataSetScalar( vs, grid ) );
+}

src/dataHandler/WDataSetScalar.h

@@ -149,6 +149,15 @@ public:
      */
     static boost::shared_ptr< WPrototyped > getPrototype();
 
+    /**
+     * Returns a new dataset with the given valueset and grid that is of the same type as this dataset.
+     *
+     * \param vs The valueset.
+     * \param grid The grid.
+     * \return The new dataset.
+     */
+    virtual boost::shared_ptr< WDataSet > clone( boost::shared_ptr< WValueSetBase > vs, boost::shared_ptr< WGrid > grid ) const;
+
 protected:
 
     /**

src/dataHandler/WDataSetSingle.cpp

@@ -169,3 +169,8 @@ double WDataSetSingle::getValueAt( size_t id ) const
 
     return 0.0; // should not be reached. Just there to quiet compiler.
 }
+
+boost::shared_ptr< WDataSet > WDataSetSingle::clone( boost::shared_ptr< WValueSetBase > vs, boost::shared_ptr< WGrid > grid ) const
+{
+    return boost::shared_ptr< WDataSet >( new WDataSetSingle( vs, grid ) );
+}

src/dataHandler/WDataSetSingle.h

@@ -176,6 +176,15 @@ public:
      */
     static boost::shared_ptr< WPrototyped > getPrototype();
 
+    /**
+     * Returns a new dataset with the given valueset and grid that is of the same type as this dataset.
+     *
+     * \param vs The valueset.
+     * \param grid The grid.
+     * \return The new dataset.
+     */
+    virtual boost::shared_ptr< WDataSet > clone( boost::shared_ptr< WValueSetBase > vs, boost::shared_ptr< WGrid > grid ) const;
+
 protected:
 
     /**

src/dataHandler/WDataSetSphericalHarmonics.cpp

@@ -150,3 +150,8 @@ bool WDataSetSphericalHarmonics::isTexture() const
 {
     return false;
 }
+
+boost::shared_ptr< WDataSet > WDataSetSphericalHarmonics::clone( boost::shared_ptr< WValueSetBase > vs, boost::shared_ptr< WGrid > grid ) const
+{
+    return boost::shared_ptr< WDataSet >( new WDataSetSphericalHarmonics( vs, grid ) );
+}

src/dataHandler/WDataSetSphericalHarmonics.h

@@ -137,6 +137,15 @@ public:
      */
     virtual bool isTexture() const;
 
+    /**
+     * Returns a new dataset with the given valueset and grid that is of the same type as this dataset.
+     *
+     * \param vs The valueset.
+     * \param grid The grid.
+     * \return The new dataset.
+     */
+    virtual boost::shared_ptr< WDataSet > clone( boost::shared_ptr< WValueSetBase > vs, boost::shared_ptr< WGrid > grid ) const;
+
 protected:
 
     /**

src/dataHandler/WDataSetTimeSeries.h

@@ -46,6 +46,7 @@ class WDataSetTimeSeriesTest;
  * A dataset that stores a time series.
  *
  * \note Only works for scalar datasets at the moment!
+ * \note this is only a temporary solution
  */
 class OWDATAHANDLER_EXPORT WDataSetTimeSeries : public WDataSet
 {

src/dataHandler/WDataSetVector.cpp

@@ -166,3 +166,8 @@ bool WDataSetVector::isTexture() const
 {
     return true;
 }
+
+boost::shared_ptr< WDataSet > WDataSetVector::clone( boost::shared_ptr< WValueSetBase > vs, boost::shared_ptr< WGrid > grid ) const
+{
+    return boost::shared_ptr< WDataSet >( new WDataSetVector( vs, grid ) );
+}

src/dataHandler/WDataSetVector.h

@@ -124,6 +124,15 @@ public:
      */
     boost::shared_ptr< WDataSetVector > isVectorDataSet();
 
+    /**
+     * Returns a new dataset with the given valueset and grid that is of the same type as this dataset.
+     *
+     * \param vs The valueset.
+     * \param grid The grid.
+     * \return The new dataset.
+     */
+    virtual boost::shared_ptr< WDataSet > clone( boost::shared_ptr< WValueSetBase > vs, boost::shared_ptr< WGrid > grid ) const;
+
 protected:
 
     /**

src/dataHandler/io/WReaderNIfTI.cpp

@@ -51,7 +51,9 @@
 #include "WReaderNIfTI.h"
 
 WReaderNIfTI::WReaderNIfTI( std::string fileName )
-    : WReader( fileName )
+    : WReader( fileName ),
+      m_sform( 4, 4 ),
+      m_qform( 4, 4 )
 {
 }
 
@@ -179,8 +181,10 @@ boost::shared_ptr< WDataSet > WReaderNIfTI::load( DataSetType dataSetType )
         throw e;
     }
 
+    m_sform = convertMatrix( header->sto_xyz );
+    m_qform = convertMatrix( header->qto_xyz );
     newGrid = boost::shared_ptr< WGridRegular3D >(
-                        new WGridRegular3D( columns, rows, frames, WGridTransformOrtho( convertMatrix( header->sto_xyz ) ) ) );
+                        new WGridRegular3D( columns, rows, frames, WGridTransformOrtho( getStandardTransform() ) ) );
 
     boost::shared_ptr< WDataSet > newDataSet;
     // known description
@@ -402,3 +406,18 @@ boost::shared_ptr< WDataSet > WReaderNIfTI::load( DataSetType dataSetType )
 
     return newDataSet;
 }
+
+wmath::WMatrix< double > WReaderNIfTI::getStandardTransform() const
+{
+    return wmath::WMatrix< double >( 4, 4 ).makeIdentity();
+}
+
+wmath::WMatrix< double > WReaderNIfTI::getSFormTransform() const
+{
+    return m_sform;
+}
+
+wmath::WMatrix< double > WReaderNIfTI::getQFormTransform() const
+{
+    return m_qform;
+}

src/dataHandler/io/WReaderNIfTI.h

@@ -64,6 +64,27 @@ public:
      */
     virtual boost::shared_ptr< WDataSet > load( DataSetType dataSetType = W_DATASET_NONE  );
 
+    /**
+     * Returns a standard transformation.
+     *
+     * \return A Wmatrix that represents the dataset's transformation.
+     */
+    wmath::WMatrix< double > getStandardTransform() const;
+
+    /**
+     * Returns the SForm transformation stored in the nifti file's header.
+     *
+     * \return A Wmatrix that represents the dataset's transformation.
+     */
+    wmath::WMatrix< double > getSFormTransform() const;
+
+    /**
+     * Returns the QForm transformation stored in the nifti file's header.
+     *
+     * \return A Wmatrix that represents the dataset's transformation.
+     */
+    wmath::WMatrix< double > getQFormTransform() const;
+
 protected:
 private:
     /**
@@ -81,6 +102,12 @@ private:
      * \param in this matrix will be converted.
      */
     wmath::WMatrix< double > convertMatrix( const mat44& in );
+
+    //! the sform transform stored in the file header
+    wmath::WMatrix< double > m_sform;
+
+    //! the qform transform stored in the file header
+    wmath::WMatrix< double > m_qform;
 };
 
 #endif  // WREADERNIFTI_H

src/kernel/modules/data/WMData.cpp

@@ -33,6 +33,7 @@
 #include "../../../dataHandler/WDataSetScalar.h"
 #include "../../../dataHandler/WDataSetTimeSeries.h"
 #include "../../../dataHandler/WDataSetVector.h"
+#include "../../../dataHandler/WDataSetRawHARDI.h"
 #include "../../../dataHandler/WSubject.h"
 #include "../../../dataHandler/WDataHandler.h"
 #include "../../../dataHandler/WDataTexture3D.h"
@@ -54,7 +55,10 @@
 WMData::WMData():
     WModule(),
     m_fileNameSet( false ),
-    m_isTexture()
+    m_isTexture(),
+    m_transformNoMatrix( 4, 4 ),
+    m_transformSForm( 4, 4 ),
+    m_transformQForm( 4, 4 )
 {
     // initialize members
 }
@@ -124,88 +128,26 @@ void WMData::connectors()
 
 void WMData::properties()
 {
-    // properties
+    m_propCondition = boost::shared_ptr< WCondition >( new WCondition() );
 
+    // properties
     m_dataName = m_infoProperties->addProperty( "Filename", "The filename of the dataset.", std::string( "" ) );
     m_dataType = m_infoProperties->addProperty( "Data type", "The type of the the single data values.", std::string( "" ) );
 
-    // use this callback for the other properties
-    WPropertyBase::PropertyChangeNotifierType propertyCallback = boost::bind( &WMData::propertyChanged, this, _1 );
-
-    // { TODO(ebaum): this is deprecated and will be replaced by WGEColormapping
-    m_groupTex = m_properties->addPropertyGroup( "Texture Properties ",  "Properties only related to the texture representation." );
-
-    // several other properties
-    m_interpolation = m_groupTex->addProperty( "Interpolation",
-                                                  "If active, the boundaries of single voxels"
-                                                  " will not be visible in colormaps. The transition between"
-                                                  " them will be smooth by using interpolation then.",
-                                                  true,
-                                                  propertyCallback );
-    m_threshold = m_groupTex->addProperty( "Threshold", "Values below this threshold will not be "
-                                              "shown in colormaps.", 0.0, propertyCallback );
-    m_threshold->setMax( 1.0 );
-    m_threshold->setMin( 0.0 );
-
-    m_opacity = m_groupTex->addProperty( "Opacity %", "The opacity of this data in colormaps combining"
-                                            " values from several data sets.", 100, propertyCallback );
-    m_opacity->setMax( 100 );
-    m_opacity->setMin( 0 );
-
-    m_colorMapSelectionsList = boost::shared_ptr< WItemSelection >( new WItemSelection() );
-    m_colorMapSelectionsList->addItem( "Grayscale", "" );
-    m_colorMapSelectionsList->addItem( "Rainbow", "" );
-    m_colorMapSelectionsList->addItem( "Hot iron", "" );
-    m_colorMapSelectionsList->addItem( "Negative to positive", "" );
-    m_colorMapSelectionsList->addItem( "Atlas", "" );
-    m_colorMapSelectionsList->addItem( "Blue-Green-Purple", "" );
-    m_colorMapSelectionsList->addItem( "Vector", "" );
-
-    m_colorMapSelection = m_groupTex->addProperty( "Colormap",  "Colormap type.", m_colorMapSelectionsList->getSelectorFirst(), propertyCallback );
-    WPropertyHelper::PC_SELECTONLYONE::addTo( m_colorMapSelection );
-
     m_matrixSelectionsList = boost::shared_ptr< WItemSelection >( new WItemSelection() );
     m_matrixSelectionsList->addItem( "No matrix", "" );
-    m_matrixSelectionsList->addItem( "qform", "" );
     m_matrixSelectionsList->addItem( "sform", "" );
+    m_matrixSelectionsList->addItem( "qform", "" );
 
     m_matrixSelection = m_properties->addProperty( "Transformation matrix",  "matrix",
-            m_matrixSelectionsList->getSelectorFirst(), propertyCallback );
+                                    m_matrixSelectionsList->getSelectorFirst(), m_propCondition );
     WPropertyHelper::PC_SELECTONLYONE::addTo( m_matrixSelection );
-    // }
 }
 
 void WMData::propertyChanged( boost::shared_ptr< WPropertyBase > property )
 {
     if( m_isTexture )
     {
-        // { TODO(ebaum): this is deprecated and will be replaced by WGEColormapping
-        if ( property == m_threshold )
-        {
-            m_dataSet->getTexture()->setThreshold( m_threshold->get() );
-        }
-        else if ( property == m_opacity )
-        {
-            m_dataSet->getTexture()->setOpacity( m_opacity->get() );
-        }
-        else if ( property == m_interpolation )
-        {
-            m_dataSet->getTexture()->setInterpolation( m_interpolation->get() );
-        }
-        else if ( property == m_colorMapSelection )
-        {
-            m_dataSet->getTexture()->setSelectedColormap( m_colorMapSelection->get( true ).getItemIndexOfSelected( 0 ) );
-        }
-        else if ( property == m_matrixSelection )
-        {
-            boost::shared_ptr< WGridRegular3D > grid = m_dataSet->getTexture()->getGrid();
-
-            //grid->setActiveMatrix( m_matrixSelection->get( true ).getItemIndexOfSelected( 0 ) );
-
-            WDataHandler::getDefaultSubject()->getChangeCondition()->notify();
-            m_output->triggerUpdate();
-        }
-        // }
         if ( property == m_active )
         {
             // forward to texture
@@ -249,6 +191,9 @@ void WMData::notifyStop()
 
 void WMData::moduleMain()
 {
+    m_moduleState.setResetable( true, true );
+    m_moduleState.add( m_propCondition );
+
     WAssert( m_fileNameSet, "No filename specified." );
 
     using wiotools::getSuffix;
@@ -266,17 +211,6 @@ void WMData::moduleMain()
     // load it now
     std::string suffix = getSuffix( fileName );
 
-    // { TODO(ebaum): this is deprecated and will be replaced by WGEColormapping
-    if( suffix == ".fib"
-        || suffix == ".cnt"
-        || suffix == ".asc"
-        || suffix == ".edf" )
-    {
-        // hide other properties since they make no sense fo these data set types.
-        m_groupTex->setHidden();
-    }
-    // }
-
     if( suffix == ".nii"
         || ( suffix == ".gz" && ::nifti_compiled_with_zlib() ) )
     {
@@ -290,6 +224,10 @@ void WMData::moduleMain()
 
         WReaderNIfTI niiLoader( fileName );
         m_dataSet = niiLoader.load();
+        m_transformNoMatrix = niiLoader.getStandardTransform();
+        m_transformSForm = niiLoader.getSFormTransform();
+        m_transformQForm = niiLoader.getQFormTransform();
+
         m_isTexture = m_dataSet->isTexture();
 
         boost::shared_ptr< WDataSetSingle > dss = boost::shared_dynamic_cast< WDataSetSingle >( m_dataSet );
@@ -301,9 +239,6 @@ void WMData::moduleMain()
                 case W_DT_UNSIGNED_CHAR:
                 case W_DT_INT16:
                 case W_DT_SIGNED_INT:
-                    // { TODO(ebaum): this is deprecated and will be replaced by WGEColormapping
-                    m_colorMapSelection->set( m_colorMapSelectionsList->getSelector( 0 ) );
-                    // }
                     m_dataSet->getTexture2()->colormap()->set(
                         m_dataSet->getTexture2()->colormap()->get().newSelector( WItemSelector::IndexList( 1, 0 ) )
                     );
@@ -312,10 +247,6 @@ void WMData::moduleMain()
                 case W_DT_DOUBLE:
                     if( boost::shared_dynamic_cast< WDataSetVector >( m_dataSet ) )
                     {
-                        // { TODO(ebaum): this is deprecated and will be replaced by WGEColormapping
-                        m_colorMapSelection->set( m_colorMapSelectionsList->getSelector( 6 ) );
-                        m_interpolation->set( false );
-                        // }
                         m_dataSet->getTexture2()->colormap()->set(
                             m_dataSet->getTexture2()->colormap()->get().newSelector( WItemSelector::IndexList( 1, 6 ) )
                         );
@@ -323,9 +254,6 @@ void WMData::moduleMain()
                     }
                     else
                     {
-                        // { TODO(ebaum): this is deprecated and will be replaced by WGEColormapping
-                        m_colorMapSelection->set( m_colorMapSelectionsList->getSelector( 5 ) );
-                        // }
                         m_dataSet->getTexture2()->colormap()->set(
                             m_dataSet->getTexture2()->colormap()->get().newSelector( WItemSelector::IndexList( 1, 5 ) )
                         );
@@ -335,15 +263,6 @@ void WMData::moduleMain()
                     WAssert( false, "Unknow data type in Data module" );
             }
         }
-
-        // { TODO(ebaum): this is deprecated and will be replaced by WGEColormapping
-        if( boost::shared_dynamic_cast< WDataSetScalar >( m_dataSet ) )
-        {
-            m_threshold->setMin( boost::shared_dynamic_cast< WDataSetScalar >( m_dataSet )->getMin() );
-            m_threshold->setMax( boost::shared_dynamic_cast< WDataSetScalar >( m_dataSet )->getMax() );
-            m_threshold->set( boost::shared_dynamic_cast< WDataSetScalar >( m_dataSet )->getMin() );
-        }
-        // }
     }
     else if( suffix == ".edf" )
     {
@@ -394,22 +313,69 @@ void WMData::moduleMain()
     // I am interested in the active property ( manually subscribe signal )
     m_active->getCondition()->subscribeSignal( boost::bind( &WMData::propertyChanged, this, m_active ) );
 
-    // { TODO(ebaum): this is deprecated and will be replaced by WGEColormapping
-    // register at datahandler
-    WDataHandler::registerDataSet( m_dataSet ); // this will get obsolete soon
-    // }
-
     // notify
     m_output->updateData( m_dataSet );
     ready();
 
-    // go to idle mode
-    waitForStop();  // WThreadedRunner offers this for us. It uses boost::condition to avoid wasting CPU cycles with while loops.
+    while( !m_shutdownFlag() )
+    {
+        m_moduleState.wait();
+        if( m_shutdownFlag() )
+        {
+            break;
+        }
+
+        // change transform matrix
+        if( m_matrixSelection->changed() )
+        {
+            // a new grid
+            boost::shared_ptr< WGrid > newGrid;
+            boost::shared_ptr< WDataSetSingle > ds = boost::shared_dynamic_cast< WDataSetSingle >( m_dataSet );
+            boost::shared_ptr< WGridRegular3D > oldGrid = boost::shared_dynamic_cast< WGridRegular3D >( ds->getGrid() );
+
+            switch( m_matrixSelection->get( true ).getItemIndexOfSelected( 0 ) )
+            {
+            case 0:
+                newGrid = boost::shared_ptr< WGrid >( new WGridRegular3D( oldGrid->getNbCoordsX(), oldGrid->getNbCoordsY(), oldGrid->getNbCoordsZ(),
+                                                                          WGridTransformOrtho( m_transformNoMatrix ) ) );
+                break;
+            case 1:
+                newGrid = boost::shared_ptr< WGrid >( new WGridRegular3D( oldGrid->getNbCoordsX(), oldGrid->getNbCoordsY(), oldGrid->getNbCoordsZ(),
+                                                                          WGridTransformOrtho( m_transformSForm ) ) );
+                break;
+            case 2:
+                newGrid = boost::shared_ptr< WGrid >( new WGridRegular3D( oldGrid->getNbCoordsX(), oldGrid->getNbCoordsY(), oldGrid->getNbCoordsZ(),
+                                                                          WGridTransformOrtho( m_transformQForm ) ) );
+                break;
+            }
+
+            if( boost::shared_dynamic_cast< WDataSetRawHARDI >( m_dataSet ) )
+            {
+                typedef std::vector< wmath::WVector3D > OrientationType;
+                // hardi datasets are a morre difficult case because of additional parameters
+                boost::shared_ptr< WDataSetRawHARDI > hardi = boost::shared_dynamic_cast< WDataSetRawHARDI >( m_dataSet );
+                m_dataSet = boost::shared_ptr< WDataSet >(
+                                new WDataSetRawHARDI( hardi->getValueSet(), newGrid,
+                                            boost::shared_ptr< OrientationType >( new OrientationType( hardi->getOrientations() ) ),
+                                            hardi->getDiffusionBValue() ) );
+                // TODO( reichenbach ): remove copying orientations
+            }
+            else
+            {
+                // this creates a dataset of the same type as m_dataSet without explicit knowledge of the correct type
+                m_dataSet = m_dataSet->clone( ds->getValueSet(), newGrid );
+            }
+
+            // the clone() may have returned a zero-pointer, only update if it hasn't
+            // this may happen if the clone() operation has not been implemented in the derived dataset class
+            if( m_dataSet )
+            {
+                m_output->updateData( m_dataSet );
+            }
+        }
+    }
 
     // remove dataset from datahandler
-    // { TODO(ebaum): this is deprecated and will be replaced by WGEColormapping
-    WDataHandler::deregisterDataSet( m_dataSet );
-    // }
     if ( m_dataSet->isTexture() )
     {
         m_properties->removeProperty( m_dataSet->getTexture2()->getProperties() );

src/kernel/modules/data/WMData.h

@@ -159,6 +159,9 @@ protected:
      */
     virtual void notifyStop();
 
+    //! a condition for property changes
+    boost::shared_ptr< WCondition > m_propCondition;
+
     /**
      * The filename of the dataset to load.
      */
@@ -179,28 +182,6 @@ protected:
      */
     WPropString m_dataType;
 
-    // { TODO(ebaum): this is deprecated and will be replaced by WGEColormapping
-    /**
-     * \deprecated Be aware that this will be replaced by WGEColormapping
-     * Grouping the texture display properties
-     */
-    WPropGroup    m_groupTex;
-
-    /**
-     * Interpolation?
-     */
-    WPropBool m_interpolation;
-
-    /**
-     * A list of color map selection types
-     */
-    boost::shared_ptr< WItemSelection > m_colorMapSelectionsList;
-
-    /**
-     * Selection property for color map
-     */
-    WPropSelection m_colorMapSelection;
-
     /**
      * A list of color map selection types
      */
@@ -211,18 +192,6 @@ protected:
      */
     WPropSelection m_matrixSelection;
 
-
-    /**
-     * Threshold value for this data.
-     */
-    WPropDouble m_threshold;
-
-    /**
-     * Opacity value for this data.
-     */
-    WPropInt m_opacity;
-    // }
-
     bool m_isTexture; //!< Indicates whether the loaded dataSet will be available as texture.
 
     /**
@@ -232,6 +201,16 @@ protected:
      */
     void propertyChanged( boost::shared_ptr< WPropertyBase > property );
 
+    // in case of a nifti file, there may be several transforms specified in the file
+    //! a standard transform (should be an identity transform)
+    wmath::WMatrix< double > m_transformNoMatrix;
+
+    //! a standard transform (should be an identity transform)
+    wmath::WMatrix< double > m_transformSForm;
+
+    //! a standard transform (should be an identity transform)
+    wmath::WMatrix< double > m_transformQForm;
+
 private:
 
     /**