[DOC] added missing member docu

src/dataHandler/io/WLoaderNIfTI.h

@@ -42,6 +42,11 @@ class WDataHandler;
  */
 class WLoaderNIfTI : public WLoader
 {
+/**
+ * Only UnitTests may be friends.
+ */
+friend class WLoaderNIfTITest;
+
 public:
     /**
      * Constructs a loader to be executed in its own thread and ets the data needed

src/dataHandler/io/test/WLoaderNIfTI_test.h

@@ -28,18 +28,142 @@
 #include <cxxtest/TestSuite.h>
 
 #include "../WLoaderNIfTI.h"
+#include "../../WDataHandler.h"
 
 /**
  * test class the nifti loader class
  */
 class WLoaderNIfTITest : public CxxTest::TestSuite
 {
+private: // private normally comes behind public, but I would like to make it easily visible here.
+    /**
+     * Dummy DataHandler instance
+     */
+    boost::shared_ptr< WDataHandler > m_dataHandler;
+
 public:
     /**
-     * this funtion tests something
+     * Create test environment.
+     */
+    void setUp( void )
+    {
+        m_dataHandler = boost::shared_ptr< WDataHandler >( new WDataHandler() );
+    }
+
+    /**
+     * Test instantiation with non existing file
+     */
+    void testInstantiationNonExisting( void )
+    {
+        TS_ASSERT_THROWS( WLoaderNIfTI( "no such file", m_dataHandler ), WDHIOFailure );
+    }
+
+    /**
+     * Test instantiation
+     */
+    void testInstantiation( void )
+    {
+        TS_ASSERT_THROWS_NOTHING( WLoaderNIfTI( "../fixtures/scalar_signed_short.nii.gz", m_dataHandler ) );
+        TS_ASSERT_THROWS_NOTHING( WLoaderNIfTI( "../fixtures/scalar_unsigned_char.nii.gz", m_dataHandler ) );
+        TS_ASSERT_THROWS_NOTHING( WLoaderNIfTI( "../fixtures/scalar_float.nii.gz", m_dataHandler ) );
+        TS_ASSERT_THROWS_NOTHING( WLoaderNIfTI( "../fixtures/vector_float.nii.gz", m_dataHandler ) );
+        TS_ASSERT_THROWS_NOTHING( WLoaderNIfTI( "../fixtures/symmetric_2nd_order_tensor_float.nii.gz", m_dataHandler ) );
+        TS_ASSERT_THROWS_NOTHING( WLoaderNIfTI( "../fixtures/vector_unsigned_char.nii.gz", m_dataHandler ) );
+
+        TS_ASSERT_EQUALS( m_dataHandler->getNumberOfSubjects(), 0 );
+    }
+
+    /**
+     * Test if the loaded files are really in the dataHandler
+     */
+    void testLoading( void )
+    {
+        WLoaderNIfTI loader1( "../fixtures/scalar_signed_short.nii.gz", m_dataHandler );
+        WLoaderNIfTI loader2( "../fixtures/scalar_unsigned_char.nii.gz", m_dataHandler );
+        WLoaderNIfTI loader3( "../fixtures/scalar_float.nii.gz", m_dataHandler );
+        WLoaderNIfTI loader4( "../fixtures/vector_float.nii.gz", m_dataHandler );
+        WLoaderNIfTI loader5( "../fixtures/symmetric_2nd_order_tensor_float.nii.gz", m_dataHandler );
+        WLoaderNIfTI loader6( "../fixtures/vector_unsigned_char.nii.gz", m_dataHandler );
+
+        TS_ASSERT_EQUALS( m_dataHandler->getNumberOfSubjects(), 0 );
+
+        loader1.load();
+
+        TS_ASSERT_EQUALS( m_dataHandler->getNumberOfSubjects(), 1 );
+        TS_ASSERT_EQUALS( m_dataHandler->getSubject( 0 )->getNumberOfDataSets(), 1 );
+
+        loader2.load();
+
+        TS_ASSERT_EQUALS( m_dataHandler->getNumberOfSubjects(), 1 );
+        TS_ASSERT_EQUALS( m_dataHandler->getSubject( 0 )->getNumberOfDataSets(), 2 );
+
+        loader3.load();
+
+        TS_ASSERT_EQUALS( m_dataHandler->getNumberOfSubjects(), 1 );
+        TS_ASSERT_EQUALS( m_dataHandler->getSubject( 0 )->getNumberOfDataSets(), 3 );
+
+        loader4.load();
+
+        TS_ASSERT_EQUALS( m_dataHandler->getNumberOfSubjects(), 1 );
+        TS_ASSERT_EQUALS( m_dataHandler->getSubject( 0 )->getNumberOfDataSets(), 4 );
+
+        loader5.load();
+
+        TS_ASSERT_EQUALS( m_dataHandler->getNumberOfSubjects(), 1 );
+        TS_ASSERT_EQUALS( m_dataHandler->getSubject( 0 )->getNumberOfDataSets(), 5 );
+
+        loader6.load();
+
+        TS_ASSERT_EQUALS( m_dataHandler->getNumberOfSubjects(), 1 );
+        TS_ASSERT_EQUALS( m_dataHandler->getSubject( 0 )->getNumberOfDataSets(), 6 );
+    }
+
+    /**
+     * Test conversion of nifti matrix to OW matrix.
      */
-    void testSomething( void )
+    void testMatrixConversion( void )
     {
+        mat44 dummy;
+        dummy.m[0][0] = 1.1;
+        dummy.m[0][1] = 1.2;
+        dummy.m[0][2] = 1.3;
+        dummy.m[0][3] = 1.4;
+        dummy.m[1][0] = 1.5;
+        dummy.m[1][1] = 1.6;
+        dummy.m[1][2] = 1.7;
+        dummy.m[1][3] = 1.8;
+        dummy.m[2][0] = 1.9;
+        dummy.m[2][1] = 1.11;
+        dummy.m[2][2] = 1.12;
+        dummy.m[2][3] = 1.13;
+        dummy.m[3][0] = 1.14;
+        dummy.m[3][1] = 1.15;
+        dummy.m[3][2] = 1.16;
+        dummy.m[3][3] = 1.17;
+
+        WLoaderNIfTI loader1( "../fixtures/scalar_signed_short.nii.gz", m_dataHandler );
+        wmath::WMatrix< double >  result = loader1.convertMatrix( dummy );
+
+        TS_ASSERT_EQUALS( result.getNbRows(), 4 );
+        TS_ASSERT_EQUALS( result.getNbCols(), 4 );
+
+        double delta = 1e-7;
+        TS_ASSERT_DELTA( result( 0, 0 ), 1.1, delta );
+        TS_ASSERT_DELTA( result( 0, 1 ), 1.2, delta );
+        TS_ASSERT_DELTA( result( 0, 2 ), 1.3, delta );
+        TS_ASSERT_DELTA( result( 0, 3 ), 1.4, delta );
+        TS_ASSERT_DELTA( result( 1, 0 ), 1.5, delta );
+        TS_ASSERT_DELTA( result( 1, 1 ), 1.6, delta );
+        TS_ASSERT_DELTA( result( 1, 2 ), 1.7, delta );
+        TS_ASSERT_DELTA( result( 1, 3 ), 1.8, delta );
+        TS_ASSERT_DELTA( result( 2, 0 ), 1.9, delta );
+        TS_ASSERT_DELTA( result( 2, 1 ), 1.11, delta );
+        TS_ASSERT_DELTA( result( 2, 2 ), 1.12, delta );
+        TS_ASSERT_DELTA( result( 2, 3 ), 1.13, delta );
+        TS_ASSERT_DELTA( result( 3, 0 ), 1.14, delta );
+        TS_ASSERT_DELTA( result( 3, 1 ), 1.15, delta );
+        TS_ASSERT_DELTA( result( 3, 2 ), 1.16, delta );
+        TS_ASSERT_DELTA( result( 3, 3 ), 1.17, delta );
     }
 };
 

src/gui/qt4/WQt4Gui.cpp

@@ -81,7 +81,15 @@ boost::program_options::variables_map parseOptions( int argc, char** argv )
 
 int WQt4Gui::run()
 {
-    m_optionsMap = parseOptions( argc, argv );
+    try
+    {
+        m_optionsMap = parseOptions( argc, argv );
+    }
+    catch( boost::program_options::unknown_option e )
+    {
+        std::cout << e.what() << std::endl;
+        return 1;
+    }
 
     // exit as fast as possible if command line asks for help.
     if( m_optionsMap.count( "help" ) )

src/kernel/WKernel.cpp

@@ -132,8 +132,9 @@ void WKernel::threadMain()
     m_graphicsEngine->run();
 
     // default modules
-    m_moduleContainer->add( m_moduleFactory->create( m_moduleFactory->getPrototypeByName( "Navigation Slice Module" ) ) , true );
+//    m_moduleContainer->add( m_moduleFactory->create( m_moduleFactory->getPrototypeByName( "Navigation Slice Module" ) ) , true );
     m_moduleContainer->add( m_moduleFactory->create( m_moduleFactory->getPrototypeByName( "Coordinate System Module" ) ) , true );
+    m_moduleContainer->add( m_moduleFactory->create( m_moduleFactory->getPrototypeByName( "Marching Cubes" ) ) , true );
 
     // actually there is nothing more to do here
     waitForStop();

src/math/WMatrix.hpp

@@ -118,7 +118,7 @@ public:
 
 protected:
 private:
-    size_t m_nbCols;
+    size_t m_nbCols; //!< Number of columns of the matrix. The number of rows will be computed by (size/m_nbCols).
 };
 }  // End of namespace
 #endif  // WMATRIX_H