* And now, real code to write pngs!

AMDiS/src/BasisFunction.h

@@ -362,9 +362,7 @@ namespace AMDiS {
     virtual void  coarseRestr(DOFVector<WorldVector<double> >*, RCNeighbourList*, int)
     {}
 
-    /** \brief
-     * Returns local dof indices of the element for the given fe space.
-     */
+    /// Returns local dof indices of the element for the given fe space.
     virtual const DegreeOfFreedom *getLocalIndices(const Element*,
 						   const DOFAdmin*,
 						   DegreeOfFreedom*) const
@@ -372,9 +370,7 @@ namespace AMDiS {
       return NULL;
     }
 
-    /** \brief
-     * Returns local dof indices of the element for the given fe space.
-     */
+    /// Returns local dof indices of the element for the given fe space.
     virtual void getLocalIndicesVec(const Element*,
 				    const DOFAdmin*,
 				    Vector<DegreeOfFreedom>*) const

AMDiS/src/DOFMatrix.cc

-#include "DOFMatrix.h"
 #include <algorithm>
 #include <png.h>
+
+#include "DOFMatrix.h"
 #include "QPsiPhi.h"
 #include "BasisFunction.h"
 #include "Boundary.h"
@@ -754,7 +755,8 @@ namespace AMDiS {
 
   void DOFMatrix::createPictureFile(const char* filename, int dim)
   {
-    png_structp png_ptr = png_create_write_struct(PNG_LIBPNG_VER_STRING, NULL, NULL, NULL);
+    png_structp png_ptr = png_create_write_struct(PNG_LIBPNG_VER_STRING, 
+						  NULL, NULL, NULL);
 
     if (!png_ptr)
        return;
@@ -763,9 +765,8 @@ namespace AMDiS {
     for (int i = 0; i < dim; i++) {
       rowPointers[i] = (png_byte*)png_malloc(png_ptr, dim);
 
-      for (int j = 0; j < dim; j++) {
+      for (int j = 0; j < dim; j++)
 	rowPointers[i][j] = 255;
-      }
     }
 
     double scalFactor = static_cast<double>(dim) / static_cast<double>(matrix.size());

AMDiS/src/DataCollector.h

@@ -42,17 +42,14 @@ namespace AMDiS {
    * \ingroup Output
    *
    * \brief
-   * Provides data collecting of element, vertex and value data 
-   * for file writers.
+   * Provides data collecting of element, vertex and value data for file writer.
    */
   class DataCollector 
     {
     public:
       MEMORY_MANAGED(DataCollector);
 
-      /** \brief
-       * Constructor.
-       */
+      /// Constructor
       DataCollector(const FiniteElemSpace *feSpace,
 		    DOFVector<double> *values,
 		    int level = -1,
@@ -61,156 +58,96 @@ namespace AMDiS {
 
       ~DataCollector();
 
-      /** \brief
-       * Fills the DataCollector with all possible datas.
-       */
+      /// Fills the DataCollector with all possible datas.
       void fillAllData();
 
-      /** \brief
-       * Returns list with element information.
-       */
+      /// Returns list with element information.
       std::list<ElementInfo>* getElementInfos();
 
-      /** \brief
-       * Returns vector with vertex information.
-       */
+      /// Returns vector with vertex information.
       DOFVector< std::list<VertexInfo> >* getVertexInfos();
 
-      /** \brief
-       * Returns the finite element space of the problem.
-       */
+      /// Returns the finite element space of the problem.
       const FiniteElemSpace* getFeSpace();
 
-      /** \brief
-       * Returns vector with value information.
-       */     
+      /// Returns vector with value information.
       DOFVector<double>* getValues();
 
-      /** \brief
-       * Returns vector with information about dof coordinates.
-       */     
+      /// Returns vector with information about dof coordinates.
       DOFVector< std::list<WorldVector<double> > >* getDofCoords();
 
-      /** \brief
-       * Returns vector with information about interpolation 
-       * point indexing.
-       */          
+      /// Returns vector with information about interpolation point indexing.
       DOFVector<int>* getInterpPointInd();
 
-      /** \brief
-       *
-       */
+      ///
       DOFVector< std::list<WorldVector<double> > >* getInterpPointCoords();
 
-      /** \brief
-       * Returns list of interpolation point information.
-       */
+      /// Returns list of interpolation point information.
       std::vector< std::vector<int> >* getInterpPoints();
 
-      /** \brief
-       * Returns list of information about periodics.
-       */
+      /// Returns list of information about periodics.
       std::list<PeriodicInfo>* getPeriodicInfos();
 
-      /** \brief
-       * Returns the number of vertices.
-       */
+      /// Returns the number of vertices.
       int getNumberVertices();
 
-      /** \brief
-       * Returns the number of elements.
-       */
+      /// Returns the number of elements.
       int getNumberElements();
 
-      /** \brief
-       * Returns the number of interpolation points.
-       */
+      /// Returns the number of interpolation points.
       int getNumberInterpPoints();
 
-      /** \brief
-       * Returns the number of connections.
-       */
+      // Returns the number of connections.
       int getNumberConnections();
       
-      /** \brief
-       * Returns the mesh of the problem.
-       */
+      /// Returns the mesh of the problem.
       Mesh* getMesh();
 
       void setMesh(Mesh *mesh) {
 	mesh_ = mesh;
-      };
+      }
 
     protected:  
-      /** \brief
-       * Start collecting element and vertex data of the problem.
-       */
+      /// Start collecting element and vertex data of the problem.
       int startCollectingElementData();
 
-      /** \brief
-       * Start collecting value data of the problem.
-       */
+      /// Start collecting value data of the problem.
       int startCollectingValueData();
 
-      /** \brief
-       * Start collecting periodic data of the problem.
-       */
+      /// Start collecting periodic data of the problem.
       int startCollectingPeriodicData();
 
-      /** \brief
-       * Adds information about one element and its vertices.
-       */
+      /// Adds information about one element and its vertices.
       int addElementData(ElInfo* elInfo);
 
-      /** \brief
-       * Adds value information of one element.
-       */
+      /// Adds value information of one element.
       int addValueData(ElInfo *elInfo);
 
-      /** \brief
-       * Adds information about interpolation points of vertices.
-       */
+      /// Adds information about interpolation points of vertices.
       int addInterpData(ElInfo *elInfo);
 
-      /** \brief
-       * Adds value information of one element.
-       */
+      /// Adds value information of one element.
       int addPeriodicData(ElInfo *elInfo);
 
-
-      /** \brief
-       * Vector with vertex values
-       */
+      /// Vector with vertex values
       DOFVector<double> *values_;
 
-      /** \brief
-       * Level information for traversing the mesh.
-       */
+      /// Level information for traversing the mesh.
       int level_;
 
-      /** \brief
-       * Flags for traversing the mesh.
-       */
+      /// Flags for traversing the mesh.
       Flag traverseFlag_;
 
-      /** \brief
-       * 
-       */
+      ///
       const FiniteElemSpace *feSpace_;
 
-      /** \brief
-       * Mesh that should be written
-       */
+      /// Mesh that should be written
       Mesh *mesh_;
       
-      /** \brief
-       * DOFAdmin of values
-       */
+      /// DOFAdmin of values
       DOFAdmin *localAdmin_;
 
-      /** \brief
-       * vertex pre-dofs
-       */
+      /// vertex pre-dofs
       int nPreDofs_;
 
       /// Number of vertices.

AMDiS/src/ElInfo.h

@@ -101,57 +101,42 @@ namespace AMDiS {
       return *this;
     }
 
-    // ===== getting-methods ======================================================
   public:
     /** \name getting methods
      * \{ 
      */
 
-    /** \brief
-     * Get ElInfo's \ref mesh_
-     */
+    /// Get ElInfo's \ref mesh_
     inline Mesh* getMesh() const { 
       return mesh_; 
     }
 
-    /** \brief
-     * Get ElInfo's \ref macroElement_
-     */
+    /// Get ElInfo's \ref macroElement_
     inline MacroElement* getMacroElement() const { 
       return macroElement_; 
     }
 
-    /** \brief
-     * Get ElInfo's \ref element
-     */
+    /// Get ElInfo's \ref element
     inline Element* getElement() const { 
       return element_; 
     }
 
-    /** \brief
-     * Get ElInfo's \ref parent_
-     */
+    /// Get ElInfo's \ref parent_
     inline Element* getParent() const { 
       return parent_; 
     }
 
-    /** \brief
-     * Get ElInfo's \ref fillFlag_
-     */
+    /// Get ElInfo's \ref fillFlag_
     inline Flag getFillFlag() const { 
       return fillFlag_; 
     }
 
-    /** \brief
-     * Get ElInfo's \ref level
-     */
+    /// Get ElInfo's \ref level
     inline int getLevel() const { 
       return level; 
     }
 
-    /** \brief
-     * Get ElInfo's \ref iChild
-     */ 
+    /// Get ElInfo's \ref iChild
     inline int getIChild() const {
       return iChild;
     }
@@ -188,12 +173,10 @@ namespace AMDiS {
       return coord_; 
     }
 
-    /** \brief
-     * Get ElInfo's \ref oppCoord_[i]
-     */
+    /// Get ElInfo's \ref oppCoord_[i]
     inline WorldVector<double>& getOppCoord(int i) { 
       return oppCoord_[i]; 
-    };
+    }
 
     /** \brief
      * Get ElInfo's \ref boundary_[i] 
@@ -466,20 +449,13 @@ namespace AMDiS {
 				     int iChild) const = 0;
 
   protected:
-
-    /** \brief
-     *  Pointer to the current mesh
-     */
+    /// Pointer to the current mesh
     Mesh *mesh_;
 
-    /** \brief 
-     * Pointer to the current element
-     */
+    /// Pointer to the current element
     Element *element_;
 
-    /** \brief 
-     * \ref element is child of element parent_
-     */
+    /// \ref element is child of element parent_
     Element *parent_;
 
     /** \brief 

AMDiS/src/ElementMatrix.h

@@ -27,10 +27,6 @@
 
 namespace AMDiS {
 
-  // =============================================================================
-  // ===== class ElementMatrix ===================================================
-  // =============================================================================
-
   /** \ingroup Assembler
    *  
    * \brief
@@ -42,24 +38,18 @@ namespace AMDiS {
   public:
     MEMORY_MANAGED(ElementMatrix);
 
-    /** \brief
-     * Constructor.
-     */
+    /// Constructor
     ElementMatrix(int numRows, int numCols) 
       : Matrix<double>(numRows, numCols),
 	rowIndices(numRows),
 	colIndices(numCols)
-    {};
+    {}
 
   public:
-    /** \brief
-     * row dof indices.
-     */
+    /// Row dof indices.
     Vector<DegreeOfFreedom> rowIndices;
 
-    /** \brief
-     * column dof indices.
-     */
+    /// Column dof indices.
     Vector<DegreeOfFreedom> colIndices;
   };
 

AMDiS/src/FileWriter.cc

@@ -108,6 +108,7 @@ namespace AMDiS {
     writeParaViewAnimation = 0;
     writePeriodicFormat = 0;
     writePngFormat = 0;
+    pngType = 0;
     appendIndex = 0;
     indexLength = 5;
     indexDecimals = 3;
@@ -135,6 +136,7 @@ namespace AMDiS {
     GET_PARAMETER(0, name + "->Periodic format", "%d", &writePeriodicFormat);
     GET_PARAMETER(0, name + "->Periodic ext", &periodicFileExt);
     GET_PARAMETER(0, name + "->PNG format", "%d", &writePngFormat);
+    GET_PARAMETER(0, name + "->PNG type", "%d", &pngType);
     GET_PARAMETER(0, name + "->append index", "%d", &appendIndex);
     GET_PARAMETER(0, name + "->index length", "%d", &indexLength);
     GET_PARAMETER(0, name + "->index decimals", "%d", &indexDecimals);
@@ -233,14 +235,14 @@ namespace AMDiS {
       VtkWriter vtkWriter(&dataCollectors);
       vtkWriter.updateAnimationFile(fn + paraViewFileExt, 
 				    &paraViewAnimationFrames_, 
-				    const_cast<char*>((filename + ".pvd").c_str()));
+				    filename + ".pvd");
     }
 
     if (writePngFormat) {
       PngWriter pngWriter(dataCollectors[0]);
-      pngWriter.writeFile(const_cast<char*>((fn + paraViewFileExt).c_str()));
+      pngWriter.writeFile(fn + ".png", pngType);
 
-      MSG("PNG image file written to %s\n", (fn + paraViewFileExt).c_str());
+      MSG("PNG image file written to %s\n", (fn + ".png").c_str());
     }
     
 

AMDiS/src/FileWriter.h

@@ -184,6 +184,9 @@ namespace AMDiS {
     /// 0: Don't write png files; 1: Write png image files.
     int writePngFormat;
 
+    /// 0: Gray color picture; 1: RGB picture.
+    int pngType;
+
     /** \brief
      * 0: Don't append time index to filename prefix.
      * 1: Append time index to filename prefix.

AMDiS/src/FiniteElemSpace.h

@@ -32,10 +32,6 @@
 
 namespace AMDiS {
 
-  // ============================================================================
-  // ===== forward declarations =================================================
-  // ============================================================================
-
   class DOFAdmin;
   class BasisFunction;
   class Mesh;
@@ -43,29 +39,19 @@ namespace AMDiS {
   template<typename T> class DOFVector;
   template<typename T> class DimVec;
 
-  // ============================================================================
-  // ===== class FiniteElemSpace ================================================
-  // ============================================================================
-
   /** \ingroup FEMSpace