[MERGE] with 58e7b29fbe6a1cf708b149b04ea9dbc9d29577b5

src/CMakeLists.txt

@@ -175,7 +175,6 @@ ENDIF()
 IF( ITK_FOUND AND OW_USE_ITK )
 	SET( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DOW_USE_ITK" CACHE STRING "" FORCE )
 	SET( CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -DOW_USE_ITK" CACHE STRING "" FORCE )
-    SET( ITK_LIBRARIES "ITKCommon" )
 ENDIF( ITK_FOUND AND OW_USE_ITK )
 
 SET( CMAKE_CXX_FLAGS_RELWITHDEBINFO "-g -DDEBUG -O2" CACHE STRING "" FORCE )

src/dataHandler/test/WITKImageConversion_test.h

@@ -45,7 +45,7 @@ static WLogger logger;
 static bool loggerInitialized = false;
 
 /**
- * Test important functionality of WDataHandler class
+ * Test functionality of WITKConversion class.
  */
 class WITKImageConversionTest : public CxxTest::TestSuite
 {

src/modules/scalarSegmentation/CMakeLists.txt

@@ -10,8 +10,11 @@ SET( MODULE_NAME    "OWmodule_${MODULE_NAME}" )      # prefix all module names w
 
 # Build module lib
 ADD_LIBRARY( ${MODULE_NAME} SHARED ${MODULES_SRC} )
-TARGET_LINK_LIBRARIES( ${MODULE_NAME} OWkernel )
-
+IF( ITK_FOUND AND OW_USE_ITK )
+    TARGET_LINK_LIBRARIES( ${MODULE_NAME} OWkernel ${ITK_LIBRARIES})
+ELSE()
+    TARGET_LINK_LIBRARIES( ${MODULE_NAME} OWkernel )
+ENDIF()    
 IF(MSVC_IDE)
 	SET_TARGET_PROPERTIES( ${MODULE_NAME} PROPERTIES PREFIX "../")    
 ENDIF(MSVC_IDE)

src/modules/scalarSegmentation/WMScalarSegmentation.cpp

@@ -90,6 +90,7 @@ void WMScalarSegmentation::properties()
     m_algos = boost::shared_ptr< WItemSelection >( new WItemSelection );
     m_algos->addItem( "Simple Threshold", "" );
     m_algos->addItem( "Watershed", "" );
+    m_algos->addItem( "Otsu Threshold", "" );
 
     m_algoType = m_properties->addProperty( "Seg Algo", "Choose a segmentation method.", m_algos->getSelectorFirst(), m_propCondition );
 
@@ -97,6 +98,10 @@ void WMScalarSegmentation::properties()
     m_threshold->setMax( 100.0 );
     m_threshold->setMin( 0.0 );
 
+    m_level = m_properties->addProperty( "Level", "Watershed level value for segmentation.", 10.0, m_propCondition );
+    m_level->setMax( 100.0 );
+    m_level->setMin( 0.0 );
+
     WModule::properties();
 }
 
@@ -133,24 +138,12 @@ void WMScalarSegmentation::moduleMain()
             WAssert( m_dataSet->getValueSet()->order() == 0, "" );
         }
 
-        //bool propChanged = false;
-        //if( !m_algoType->changed() )
-        //{
-            //WPVGroup::PropertyConstIterator it;
-            //for( it = m_propGroups[ m_algoIndex ]->begin(); it != m_propGroups[ m_algoIndex ]->end(); ++it )
-            //{
-                //propChanged = propChanged || it->changed();
-            //}
-        //}
-        //else
-        //{
-            //WItemSelector w = m_algoType.get( true );
-            //m_algoIndex = w.getItemIndexOfSelected( 0 );
-            //propChanged = true;
-        //}
-
-        bool propChanged = m_threshold->changed();
-        if( m_dataSet && ( dataChanged || propChanged ) )
+        bool algoChanged = m_algoType->changed();
+        WItemSelector w = m_algoType->get( true );
+        m_algoIndex = w.getItemIndexOfSelected( 0 );
+
+        bool propChanged = m_threshold->changed() || m_level->changed();
+        if( m_dataSet && ( dataChanged || propChanged || algoChanged ) )
         {
             // redo calculation
             doSegmentation();
@@ -167,11 +160,22 @@ void WMScalarSegmentation::activate()
 void WMScalarSegmentation::doSegmentation()
 {
     boost::shared_ptr< WValueSetBase > vs;
+
+    debugLog() << m_algoIndex;
+
     switch( m_algoIndex )
     {
     case 0:
         vs = m_dataSet->getValueSet()->applyFunction( SimpleSegmentation( m_threshold->get( true ) ) );
         break;
+#ifdef OW_USE_ITK
+    case 1:
+        vs = m_dataSet->getValueSet()->applyFunction( WatershedSegmentation( m_level->get( true ), m_threshold->get( true ), m_dataSet ) );
+        break;
+    case 2:
+        vs = m_dataSet->getValueSet()->applyFunction( OtsuSegmentation( m_dataSet ) );
+        break;
+#endif  // OW_USE_ITK
     default:
         errorLog() << "Invalid algorithm selected." << std::endl;
     }

src/modules/scalarSegmentation/WMScalarSegmentation.h

@@ -31,11 +31,26 @@
 #include "../../common/WItemSelection.h"
 #include "../../common/WItemSelector.h"
 
+#include "../../dataHandler/WITKImageConversion.h"
+
 #include "../../kernel/WModule.h"
 #include "../../kernel/WModuleInputData.h"
 #include "../../kernel/WModuleOutputData.h"
 #include "../../dataHandler/WDataSetScalar.h"
 
+#ifdef OW_USE_ITK
+
+#include "itkWatershedImageFilter.h"
+#include "itkOtsuThresholdImageFilter.h"
+
+// smoothing filters
+#include "itkGradientAnisotropicDiffusionImageFilter.h"
+// other
+#include "itkCastImageFilter.h"
+#include "itkGradientMagnitudeImageFilter.h"
+
+#endif  // OW_USE_ITK
+
 /**
  * First version of a module that implements 3D-image segmentation algorithms.
  *
@@ -159,6 +174,9 @@ private:
      */
     WPropDouble m_threshold;
 
+    //! The watershed level.
+    WPropDouble m_level;
+
     //! A function object that implements a simple threshold segmentation.
     class SimpleSegmentation : public boost::static_visitor< boost::shared_ptr< WValueSetBase > >
     {
@@ -186,20 +204,136 @@ private:
         //! the threshold
         double m_threshold;
     };
+
+#ifdef OW_USE_ITK
+    //!
+    class WatershedSegmentation : public boost::static_visitor< boost::shared_ptr< WValueSetBase > >
+    {
+    public:
+        /**
+         * Constructor.
+         * \param t The threshold for segmentation.
+         */
+        WatershedSegmentation( double level, double t, boost::shared_ptr< WDataSetScalar > ds ) // NOLINT
+            : m_level( level ),
+              m_threshold( t ),
+              m_dataset( ds )
+        {
+        }
+
+        /**
+         * Do the segmentation.
+         *
+         * \tparam T The integral data type.
+         * \param valueset The valueset to segment.
+         * \return A pointer to a new valueset.
+         */
+        template< typename T >
+        boost::shared_ptr< WValueSetBase > operator() ( WValueSet< T > const* ) const;
+
+    private:
+        //! the level
+        double m_level;
+        //! the threshold
+        double m_threshold;
+        //! the dataset
+        boost::shared_ptr< WDataSetScalar > m_dataset;
+    };
+
+    //!
+    class OtsuSegmentation : public boost::static_visitor< boost::shared_ptr< WValueSetBase > >
+    {
+    public:
+        /**
+         * Constructor.
+         * \param t The threshold for segmentation.
+         */
+        OtsuSegmentation( boost::shared_ptr< WDataSetScalar > ds ) // NOLINT
+            : m_dataset( ds )
+        {
+        }
+
+        /**
+         * Do the segmentation.
+         *
+         * \tparam T The integral data type.
+         * \param valueset The valueset to segment.
+         * \return A pointer to a new valueset.
+         */
+        template< typename T >
+        boost::shared_ptr< WValueSetBase > operator() ( WValueSet< T > const* v ) const;
+
+    private:
+        //! the dataset
+        boost::shared_ptr< WDataSetScalar > m_dataset;
+    };
+#endif  // OW_USE_ITK
 };
 
 template< typename T >
 boost::shared_ptr< WValueSetBase > WMScalarSegmentation::SimpleSegmentation::operator() ( WValueSet< T > const* valueset ) const
 {
     std::vector< T > values( valueset->size() );
-
     for( std::size_t k = 0; k < valueset->size(); ++k )
     {
         values[ k ] = ( static_cast< double >( valueset->getScalar( k ) ) <
                         m_threshold * ( valueset->getMaximumValue() - valueset->getMinimumValue() ) / 100.0 + valueset->getMinimumValue()
-                        ? static_cast< T >( 0 ) : static_cast< T >( 1 ) );
+                        ? static_cast< T >( 0 ) : static_cast< T >( 100 ) );
     }
     return boost::shared_ptr< WValueSet< T > >( new WValueSet< T >( 0, 1, values, DataType< T >::type ) );
 }
 
+#ifdef OW_USE_ITK
+
+template< typename T >
+boost::shared_ptr< WValueSetBase > WMScalarSegmentation::WatershedSegmentation::operator() ( WValueSet< T > const* ) const
+{
+    typedef itk::Image< T, 3 > ImgType;
+    typedef itk::Image< double, 3 > RealType;
+    typedef itk::Image< uint64_t, 3 > LabelType; // this might be a problem on 32-bit systems
+    typedef itk::Image< float, 3 > FinalType;
+
+    typedef itk::GradientAnisotropicDiffusionImageFilter< ImgType, RealType > SmoothingType;
+    typedef itk::CastImageFilter< LabelType, FinalType > CastFilter;
+    typedef itk::GradientMagnitudeImageFilter< RealType, RealType > GradFilter;
+    typedef itk::WatershedImageFilter< RealType > WaterFilter;
+
+    typename ImgType::Pointer img = makeImageFromDataSet< T >( m_dataset );
+    typename SmoothingType::Pointer sm = SmoothingType::New();
+    typename CastFilter::Pointer cf = CastFilter::New();
+    typename GradFilter::Pointer gf = GradFilter::New();
+    typename WaterFilter::Pointer ws = WaterFilter::New();
+
+    sm->SetNumberOfIterations( 10 );
+    sm->SetTimeStep( 0.0625 );
+    sm->SetConductanceParameter( 2.0 );
+    sm->SetInput( img );
+    gf->SetInput( sm->GetOutput() );
+    ws->SetInput( gf->GetOutput() );
+    ws->SetLevel( m_level / 100.0 );
+    ws->SetThreshold( m_threshold / 100.0 );
+    cf->SetInput( ws->GetOutput() );
+    cf->Update();
+    boost::shared_ptr< WDataSetScalar > res = makeDataSetFromImage< float >( cf->GetOutput() );
+    return res->getValueSet();
+}
+
+template< typename T >
+boost::shared_ptr< WValueSetBase > WMScalarSegmentation::OtsuSegmentation::operator() ( WValueSet< T > const* v ) const
+{
+    typedef itk::Image< T, 3 > ImgType;
+    typedef itk::OtsuThresholdImageFilter< ImgType, ImgType > Otsu;
+
+    typename ImgType::Pointer img = makeImageFromDataSet< T >( m_dataset );
+    typename Otsu::Pointer o = Otsu::New();
+    o->SetInput( img );
+    o->SetOutsideValue( v->getMaximumValue() );
+    o->SetInsideValue( v->getMinimumValue() );
+    o->Update();
+    boost::shared_ptr< WDataSetScalar > res = makeDataSetFromImage< T >( o->GetOutput() );
+    return res->getValueSet();
+}
+
+#endif  // OW_USE_ITK
+
 #endif  // WMSCALARSEGMENTATION_H

src/modules/subtractDataSetScalar/WMSubtractDataSetScalar.h

@@ -27,6 +27,7 @@
 
 #include <string>
 #include <vector>
+#include <algorithm>
 
 #include "../../kernel/WModule.h"
 #include "../../kernel/WModuleInputData.h"
@@ -143,7 +144,7 @@ void WMSubtractDataSetScalar::subtractTyped()
     std::vector< T > values( m_first->getGrid()->size() );
     for( std::size_t k = 0; k < m_first->getGrid()->size(); ++k )
     {
-        values[ k ] = firstValueSet->rawData()[ k ] - secondValueSet->rawData()[ k ];
+        values[ k ] = std::max( 0, firstValueSet->rawData()[ k ] - secondValueSet->rawData()[ k ] );
     }
     VSPtr vs( new VS( 0, 1, values, DataType< T >::type ) );
     m_result = boost::shared_ptr< WDataSetScalar >( new WDataSetScalar( vs, m_first->getGrid() ) );