Merge with e21058799747fe27d7175ff6bc9a04ee84c3ec0d

src/CMakeLists.txt

@@ -201,13 +201,6 @@ ADD_CUSTOM_TARGET( vtest
                    COMMENT "Runs the test in verboseness to see what actually went wrong"
                  )
 
-#-------------------------------------------------------------------------------------------------------------
-# Removes all tests thus forcing them to be recompiled during the next "make"
-ADD_CUSTOM_TARGET( cleantest
-                   COMMAND ${CMAKE_COMMAND} -P ${PROJECT_SOURCE_DIR}/../tools/CMakeModules/RemoveGeneratedTests.cmake
-                   COMMENT "Remove all tests to force them to be recompiled"
-                 )
-
 #-------------------------------------------------------------------------------------------------------------
 # Checks if all is well to commit (aka commitCheck, cicheck)
 ADD_CUSTOM_TARGET( cicheck

src/graphicsEngine/WGECamera.h

@@ -68,8 +68,6 @@ public:
      */
     void reset();
 
-    // TODO(ebaum): add more default settings and camera setups here
-
 protected:
 
     /**

src/graphicsEngine/WGraphicsEngine.cpp

@@ -36,7 +36,6 @@
 #include "WGEViewer.h"
 
 WGraphicsEngine::WGraphicsEngine( std::string shaderPath ):
-    WThreadedRunner(),
     m_shaderPath( shaderPath )
 {
     WLogger::getLogger()->addLogMessage( "Initializing Graphics Engine", "GE", LL_DEBUG );
@@ -61,16 +60,6 @@ std::string WGraphicsEngine::getShaderPath()
     return m_shaderPath;
 }
 
-void WGraphicsEngine::threadMain()
-{
-    // TODO(ebaum): is this thread actually needed since each viewer runs in separate thread
-    // while( !m_FinishRequested )
-    // {
-        // currently a dummy
-        // sleep( 1 );
-    // }
-}
-
 boost::shared_ptr<WGEViewer> WGraphicsEngine::createViewer(
     osg::ref_ptr<WindowData> wdata, int x, int y, int width, int height, WGECamera::ProjectionMode projectionMode )
 {

src/graphicsEngine/WGraphicsEngine.h

@@ -48,7 +48,7 @@
  * engine.
  * \ingroup ge
  */
-class WGraphicsEngine: public WThreadedRunner
+class WGraphicsEngine
 {
 public:
 
@@ -98,11 +98,6 @@ protected:
      */
     osg::ref_ptr<WGEScene> m_RootNode;
 
-    /**
-     * Handler for repainting and event handling. Gets executed in separate thread.
-     */
-    virtual void threadMain();
-
     /**
      * All registered viewer.
      */

src/gui/qt4/WMainWindow.cpp

@@ -69,7 +69,7 @@ void WMainWindow::setupGUI( QMainWindow *mainWindow )
     mainWindow->setCentralWidget( m_centralwidget );
 
     std::cout << "init main gl" << std::endl;
-    boost::shared_ptr<WQtGLWidget> widget = boost::shared_ptr<WQtGLWidget>( new WQtGLWidget( mainWindow, WGECamera::PERSPECTIVE ) );
+    boost::shared_ptr<WQtGLWidget> widget = boost::shared_ptr<WQtGLWidget>( new WQtGLWidget( mainWindow, WGECamera::ORTHOGRAPHIC ) );
     m_glWidgets.push_back( widget );
     mainWindow->setCentralWidget( widget.get() );
 

src/kernel/WKernel.cpp

@@ -129,11 +129,7 @@ int WKernel::run()
 {
     WLogger::getLogger()->addLogMessage( "Starting Kernel", "Kernel", LL_DEBUG );
 
-    // TODO(ebaum): add separate graphics thread here
-    m_graphicsEngine->run();
-
     // run Gui
-    // TODO(all): clean up this option handler mess
     m_gui->run();
 
     // run? data handler stuff?
@@ -152,9 +148,6 @@ int WKernel::run()
     m_FinishRequested = true;
     m_moduleContainer->stop();
 
-    // finally GE
-    m_graphicsEngine->wait( true );
-
     // how to get QT return code from its thread?
     return 0;
 }
@@ -180,11 +173,6 @@ void WKernel::init()
 
     // initialize Datahandler
     m_dataHandler = boost::shared_ptr< WDataHandler >( new WDataHandler() );
-
-    // m_gui->createMainWindow();
-
-    // TODO(ebaum): the old way
-    // m_dataHandler->getSignalAddDataset()->connect( boost::bind( &WKernel::slotFinishLoadData, this, _1 ) );
 }
 
 bool WKernel::findAppPath()

src/kernel/WModule.cpp

@@ -109,11 +109,7 @@ void WModule::initialize()
     // doing it twice is not allowed
     if ( isInitialized() )
     {
-        // TODO(ebaum): is this really needed?
-        std::ostringstream s;
-        s << "Could not initialize connectors for Module " << getName() << ". Reason: already initialized.";
-
-        throw WModuleConnectorInitFailed( s.str() );
+        throw WModuleConnectorInitFailed( "Could not initialize connectors for Module " + getName() + ". Reason: already initialized." );
     }
 
     connectors();

src/kernel/test/WModuleConnector_test.h

@@ -260,11 +260,6 @@ public:
         createModules();
         initModules();
 
-        // init connectors
-        // TODO(ebaum): replace this with the module container, since the module container should manage this
-        // well actually this also tests the WModule::addConnector method and instantiation of WModuleInputConnector and
-        // WModuleOutputConnector.
-
         // try initializing twice
         TS_ASSERT_THROWS( m1->initialize(), WModuleConnectorInitFailed );
         TS_ASSERT( m1->isInitialized() );

src/modules/marchingCubes/WMMarchingCubes.cpp

@@ -27,6 +27,9 @@
 #include <string>
 #include <vector>
 
+#include <cmath>
+
+
 #include "WMMarchingCubes.h"
 #include "marchingCubesCaseTables.h"
 #include "WTriangleMesh.h"
@@ -571,6 +574,18 @@ void WMMarchingCubes::renderMesh( const WTriangleMesh& mesh )
 // TODO(wiebel): MC move this to a separate module in the future
 bool WMMarchingCubes::save( std::string fileName, const WTriangleMesh& triMesh ) const
 {
+    if( triMesh.getNumVertices() == 0 )
+    {
+        WLogger::getLogger()->addLogMessage( "Will not write file that contains 0 vertices.", "Marching Cubes", LL_ERROR );
+        return false;
+    }
+
+    if( triMesh.getNumTriangles() == 0 )
+    {
+        WLogger::getLogger()->addLogMessage( "Will not write file that contains 0 triangles.", "Marching Cubes", LL_ERROR );
+        return false;
+    }
+
     const char* c_file = fileName.c_str();
     std::ofstream dataFile( c_file );
 
@@ -580,10 +595,12 @@ bool WMMarchingCubes::save( std::string fileName, const WTriangleMesh& triMesh )
     }
     else
     {
-        WLogger::getLogger()->addLogMessage( "open file failed"+fileName , "Marching Cubes", LL_ERROR );
+        WLogger::getLogger()->addLogMessage( "open file failed" + fileName , "Marching Cubes", LL_ERROR );
         return false;
     }
 
+    dataFile.precision( 16 );
+
     WLogger::getLogger()->addLogMessage( "start writing file", "Marching Cubes", LL_DEBUG );
     dataFile << ( "# vtk DataFile Version 2.0\n" );
     dataFile << ( "generated using OpenWalnut\n" );
@@ -595,6 +612,11 @@ bool WMMarchingCubes::save( std::string fileName, const WTriangleMesh& triMesh )
     for ( unsigned int i = 0; i < triMesh.getNumVertices(); ++i )
     {
         point = triMesh.getVertex( i );
+        if( !( std::isfinite( point[0] ) && std::isfinite( point[1] ) && std::isfinite( point[2] ) ) )
+        {
+            WLogger::getLogger()->addLogMessage( "Will not write file from data that contains NAN or INF.", "Marching Cubes", LL_ERROR );
+            return false;
+        }
         dataFile << point[0] << " " << point[1] << " " << point[2] << "\n";
     }
 
@@ -618,7 +640,7 @@ bool WMMarchingCubes::save( std::string fileName, const WTriangleMesh& triMesh )
         dataFile << "0\n";
     }
     dataFile.close();
-    std::cout << " saving  done" << std::endl;
+    WLogger::getLogger()->addLogMessage( "saving done", "Marching Cubes", LL_DEBUG );
     return true;
 }
 
@@ -698,7 +720,6 @@ WTriangleMesh WMMarchingCubes::load( std::string fileName )
     size_t nbCells;
     size_t nbNumbers;
     ifs >> cellsMarker >> nbCells >> nbNumbers;
-    std::cout<< cellsMarker << " " << nbCells << " " << nbNumbers << std::endl;
 
     triMesh.resizeTriangles( nbCells );
     unsigned int nbCellVerts;
@@ -711,14 +732,10 @@ WTriangleMesh WMMarchingCubes::load( std::string fileName )
             WLogger::getLogger()->addLogMessage( "Number of cell vertices should be 3 but found " + nbCellVerts, "Marching Cubes", LL_ERROR );
     }
 
-
-
-
     // ----- Cell Types ---------
     char* cells_typesMarker = new char[30];
     size_t nbCellTypes;
     ifs >> cells_typesMarker >> nbCellTypes;
-    std::cout << cells_typesMarker << " .... " << nbCellTypes << std::endl;
     unsigned int cellType;
     for( unsigned int i = 0; i < nbCellTypes; ++i )
     {

src/modules/marchingCubes/test/WMMarchingCubes_test.h

@@ -26,10 +26,15 @@
 #define WMMARCHINGCUBES_TEST_H
 
 #include <vector>
+#include <string>
 
 #include <cxxtest/TestSuite.h>
 
 #include "../WMMarchingCubes.h"
+#include "../../../common/WLogger.h"
+
+static bool loggerInitialized = false;
+static WLogger logger;
 
 /**
  * Test for WMMarchingCubes
@@ -37,6 +42,7 @@
 class WMMarchingCubesTest : public CxxTest::TestSuite
 {
 public:
+
     /**
      * Ensure instatiation does not throw and does initialization right.
      */
@@ -191,11 +197,65 @@ public:
     }
 
     /**
-     * Test writing of surfaces
+     * Test rejection of surfaces with zero triangles or vertices for save
      */
-    void testSave()
+    void testSaveZero()
     {
-        // TODO(wiebel): MC need to test this for #117
+        if( !loggerInitialized )
+        {
+            std::cout << "Initialize logger." << std::endl;
+            logger.run();
+            loggerInitialized = true;
+        }
+
+        WMMarchingCubes mc;
+        WTriangleMesh triMesh;
+        std::string fileName = "/tmp/dummerNameDenSichKeinerMerkenBraucht2.vtk";
+
+        bool result = mc.save( fileName, triMesh );
+        TS_ASSERT_EQUALS( result, false ); // should return false as we did not have any vertices or triangles.
+    }
+
+    /**
+     * Test rejection of surfaces with nan or inf in coordinates for save
+     */
+    void testSaveInfinteNan()
+    {
+        if( !loggerInitialized )
+        {
+            std::cout << "Initialize logger." << std::endl;
+            logger.run();
+            loggerInitialized = true;
+        }
+
+        WMMarchingCubes mc;
+        WTriangleMesh triMesh;
+
+        const unsigned int nbPos = 10;
+        std::vector< Triangle > triangles( 0 );
+        Triangle tri;
+        for( unsigned int i = 0; i < 3; ++i )
+        {
+            tri.pointID[i] = i;
+        }
+        triangles.push_back( tri );
+
+        std::vector< wmath::WPosition > vertices( 0 );
+        for( unsigned int posId = 0; posId < nbPos; ++posId )
+        {
+            double x = posId * posId + 3.4;
+            double y = posId + 1;
+            double z = 3. /  static_cast< double >( posId ); // provide nan values by dividing with zero
+            vertices.push_back( wmath::WPosition( x, y, z ) );
+        }
+        triMesh.setVertices( vertices );
+
+        std::string fileName = "/tmp/dummerNameDenSichKeinerMerkenBraucht.vtk";
+
+        mc.save( fileName, triMesh );
+
+        bool result = mc.save( fileName, triMesh );
+        TS_ASSERT_EQUALS( result, false ); // should return false as we did not have all coordinates values finite.
     }
 
     /**
@@ -205,6 +265,66 @@ public:
     {
         // TODO(wiebel): MC need to test this for #118
     }
+
+    /**
+     * Test first saving data and the loading it back.
+     */
+    void testSaveAndLoad()
+    {
+        if( !loggerInitialized )
+        {
+            std::cout << "Initialize logger." << std::endl;
+            logger.run();
+            loggerInitialized = true;
+        }
+
+        WMMarchingCubes mc;
+        WTriangleMesh triMesh;
+
+        const unsigned int nbPos = 10;
+        const unsigned int nbTris = nbPos - 2;
+        std::vector< Triangle > triangles( 0 );
+        for( unsigned int triId = 0; triId < nbTris; ++triId )
+        {
+            Triangle tri;
+            for( unsigned int i = 0; i < 3; ++i )
+            {
+                tri.pointID[i] = triId + i;
+            }
+            triangles.push_back( tri );
+        }
+        triMesh.setTriangles( triangles );
+
+        std::vector< wmath::WPosition > vertices( 0 );
+        for( unsigned int posId = 0; posId < nbPos; ++posId )
+        {
+            double x = posId * posId + 3.4;
+            double y = posId + 1;
+            double z = 3. / static_cast< double >( posId + 1 );
+            vertices.push_back( wmath::WPosition( x, y, z ) );
+        }
+        triMesh.setVertices( vertices );
+
+        std::string fileName = "/tmp/dummerNameDenSichKeinerMerkenBraucht.vtk";
+
+        mc.save( fileName, triMesh );
+        WTriangleMesh result = mc.load( fileName );
+
+        TS_ASSERT_EQUALS( triMesh.getNumTriangles(), result.getNumTriangles() );
+        TS_ASSERT_EQUALS( triMesh.getNumVertices(), result.getNumVertices() );
+        TS_ASSERT_EQUALS( triMesh.getFastAddVertId(), result.getFastAddVertId() );
+        TS_ASSERT_EQUALS( triMesh.getFastAddTriangleId(), result.getFastAddTriangleId() );
+
+        for( unsigned int i = 0; i < nbPos; ++i)
+        {
+            for( unsigned int j = 0; j < 3; ++j)
+            {
+                double delta = 1e-5;
+                // TODO(wiebel): find out why this works only for delta=1e-5
+                TS_ASSERT_DELTA( triMesh.getVertex( i )[j], result.getVertex( i )[j], delta );
+            }
+        }
+    }
 };
 
 #endif  // WMMARCHINGCUBES_TEST_H

tools/CMakeModules/FindCxxTest.cmake

@@ -98,7 +98,7 @@ macro( CXXTEST_ADD_TEST _cxxtest_testname _cxxtest_outfname _cxxtest_testsuite )
 
     add_custom_command(
         OUTPUT  ${_cxxtest_real_outfname}
-        DEPENDS ${ARGN}
+        DEPENDS ${_cxxtest_testsuite} ${ARGN}
         COMMAND ${_cxxtest_executable}
         --error-printer -o ${_cxxtest_real_outfname} ${_cxxtest_testsuite}
     )