Reduce Doxygen warnings

Modules/AppUtil/include/mitkBaseApplication.h

@@ -37,10 +37,10 @@ namespace mitk
    * org.blueberry.osgi.applications extension point.
    *
    * This class contains many convenience methods to:
-   *  - Put the application in \emph{safe mode} which catches unhandled
+   *  - Put the application in <em>safe mode</em> which catches unhandled
    *    exceptions thrown in the Qt event loop and displays an error
    *    message.
-   *  - Put the application in \emph{single mode} which by default
+   *  - Put the application in <em>single mode</em> which by default
    *    sends the command line arguments to an already running instance
    *    of the same application instead of creating a second instance.
    *  - Add a list of library names which should be pre-loaded at
@@ -58,7 +58,7 @@ namespace mitk
    *  - getQApplication() to provide a custom QCoreApplication instance
    *
    * A simple but complete example:
-   * <code>
+   * \code
    * #include <mitkBaseApplication.h>
    *
    * int main(int argc, char* argv[])
@@ -70,7 +70,7 @@ namespace mitk
    *   // Run the workbench
    *   return app.run();
    * }
-   * </code>
+   * \endcode
    */
   class MITKAPPUTIL_EXPORT BaseApplication : public Poco::Util::Application
   {
@@ -275,7 +275,7 @@ namespace mitk
      * then the command line arguments used in starting the platform, and not consumed
      * by the platform code, are passed to the application as a <code>QStringList</code>.
      * </p>
-     * @param argument the argument passed to the application. May be <code>invalid</code>
+     * @param args the argument passed to the application. May be <code>invalid</code>
      * @return the result of running the application
      * @throws std::exception if anything goes wrong
      */

Modules/Classification/CLCore/include/mitkAbstractGlobalImageFeature.h

@@ -181,7 +181,7 @@ class MITKCLCORE_EXPORT AbstractGlobalImageFeature : public BaseData
   * @param checkParameterActivation Indicates if the features should only be calculated and added if the FeatureClass is activated in the parameters.
   * True: only append if activated in the parametes. False: always and append it.
   */
-  void CalculateAndAppendFeatures(const Image* image, const Image* mask, const Image* maskNoNAN, FeatureListType &featureList, bool checkParameterActivation = true);
+  void CalculateAndAppendFeatures(const Image* image, const Image* mask, const Image* maskNoNaN, FeatureListType &featureList, bool checkParameterActivation = true);
 
   itkSetMacro(Prefix, std::string);
   itkSetMacro(ShortName, std::string);

Modules/Classification/CLImportanceWeighting/include/mitkGeneralizedLinearModel.h

@@ -51,7 +51,7 @@ namespace mitk
     *
     * No input validation is done. The data and the learned model might not match!
     *
-    * @paaram c Column for which the data is guessed.
+    * @param c Column for which the data is guessed.
     */
     double Predict(const vnl_vector<double> &c);
 
@@ -64,7 +64,7 @@ namespace mitk
     *
     * No input validation is done. The data and the learned model might not match!
     *
-    * @paaram x Matrix for which the data is guessed.
+    * @param x Matrix for which the data is guessed.
     */
     vnl_vector<double> Predict(const vnl_matrix<double> &x);
 

Modules/Classification/CLUtilities/include/mitkCLUtil.h

@@ -46,7 +46,8 @@ class MITKCLUTILITIES_EXPORT CLUtil
 
   ///
   /// \brief InterpolateCreateCheckerboardPrediction
-  /// \param image
+  /// \param checkerboard_prediction
+  /// \param checkerboard_mask
   /// \param outimage
   ///
   static void InterpolateCheckerboardPrediction(mitk::Image::Pointer checkerboard_prediction, mitk::Image::Pointer & checkerboard_mask, mitk::Image::Pointer & outimage);
@@ -95,6 +96,7 @@ class MITKCLUTILITIES_EXPORT CLUtil
   /// \brief LogicalAndImages
   /// \param image1
   /// \param image2
+  /// \param outimage
   ///
   static void LogicalAndImages(const Image::Pointer &image1, const Image::Pointer &image2, Image::Pointer &outimage);
 
@@ -121,33 +123,30 @@ class MITKCLUTILITIES_EXPORT CLUtil
   /// \param image
   /// \param smoothed (Result is sigma1-sigma2)
   /// \param sigma1
-  /// \param sigma2
   ///
   static void LaplacianOfGaussianFilter(mitk::Image::Pointer image, mitk::Image::Pointer & smoothed, double sigma1);
 
   ///
   /// \brief SubtractGaussianFilter
   /// \param image
-  /// \param smoothed (Result is sigma1-sigma2)
-  /// \param sigma1
-  /// \param sigma2
+  /// \param out
+  /// \param sigma
   ///
   static void HessianOfGaussianFilter(mitk::Image::Pointer image, std::vector<mitk::Image::Pointer> &out, double sigma);
 
   ///
   /// \brief Local Histogram
   /// \param image
-  /// \param smoothed (Result is sigma1-sigma2)
-  /// \param sigma1
-  /// \param sigma2
+  /// \param out
+  /// \param Bins
+  /// \param NeighbourhoodSize
   ///
   static void LocalHistogram(mitk::Image::Pointer image, std::vector<mitk::Image::Pointer> &out, int Bins, int NeighbourhoodSize);
 
   ///
   /// \brief transform
   /// \param matrix
   /// \param mask
-  /// \param outimage
   ///
   template<typename TMatrixElementType>
   static mitk::Image::Pointer Transform(const Eigen::Matrix<TMatrixElementType, Eigen::Dynamic, Eigen::Dynamic> & matrix, const mitk::Image::Pointer & mask)
@@ -189,9 +188,8 @@ class MITKCLUTILITIES_EXPORT CLUtil
   }
   ///
   /// \brief TransformImageToMatrix
-  /// \param in_img
+  /// \param img
   /// \param mask
-  /// \param out_matrix
   ///
   template<typename TMatrixElementType>
   static Eigen::Matrix<TMatrixElementType, Eigen::Dynamic, Eigen::Dynamic> Transform(const mitk::Image::Pointer & img, const mitk::Image::Pointer & mask)
@@ -222,51 +220,51 @@ class MITKCLUTILITIES_EXPORT CLUtil
 
   ///
   /// \brief DilateBinary
-  /// \param BinaryImage
-  /// \param BinaryImage
-  /// \param Size of the StructuringElement
-  /// \param Dimension
+  /// \param sourceImage
+  /// \param resultImage
+  /// \param radius Size of the StructuringElement
+  /// \param d
   ///
   static void DilateBinary(mitk::Image::Pointer & sourceImage, mitk::Image::Pointer& resultImage, int radius , MorphologicalDimensions d);
 
   ///
   /// \brief ErodeBinary
-  /// \param BinaryImage
-  /// \param BinaryImage
-  /// \param Size of the StructuringElement
-  /// \param Dimension
+  /// \param sourceImage
+  /// \param resultImage
+  /// \param radius Size of the StructuringElement
+  /// \param d
   ///
   static void ErodeBinary(mitk::Image::Pointer & sourceImage, mitk::Image::Pointer& resultImage, int radius, MorphologicalDimensions d);
 
   ///
   /// \brief ClosingBinary
-  /// \param BinaryImage
-  /// \param BinaryImage
-  /// \param Size of the StructuringElement
-  /// \param Dimension
+  /// \param sourceImage
+  /// \param resultImage
+  /// \param radius Size of the StructuringElement
+  /// \param d
   ///
   static void ClosingBinary(mitk::Image::Pointer & sourceImage, mitk::Image::Pointer& resultImage, int radius, MorphologicalDimensions d);
 
 
   ///
   /// \brief MergeLabels
-  /// \param MultilabelImage
+  /// \param img
   /// \param map merge instruction where each map entry defines a mapping instruction. Key \c \<sourcelabel\> - Value \c \<targetlabel\>
   ///
   static void MergeLabels(mitk::Image::Pointer & img, const std::map<unsigned int, unsigned int> & map);
 
   ///
   /// \brief ConnectedComponentsImage
-  /// \param BinaryImage
-  /// \param BinaryImage
-  /// \param MultilabelImage
-  /// \param Number of components found in the image
+  /// \param image
+  /// \param mask
+  /// \param outimage
+  /// \param num_components Number of components found in the image
   ///
   static void ConnectedComponentsImage(mitk::Image::Pointer & image, mitk::Image::Pointer& mask, mitk::Image::Pointer &outimage, unsigned int& num_components);
 
   ///
   /// \brief GrabLabel
-  /// \param MultiLabelImage
+  /// \param image
   /// \param outimage
   /// \param label
   ///

Modules/Classification/DataCollection/DataHolder/mitkDataCollection.h

@@ -73,10 +73,9 @@ namespace mitk
     * @brief AddData Add a data item
     * @param data Images/Fibers/DataCollections
     * @param name name that allows identifying this data (e.g. a category T2, Segmentation , etc ...)
-    * @param description
+    * @param filePath
     * @return
     */
-
     size_t AddData(DataObject::Pointer data, std::string name, std::string filePath = "");
 
     /**
@@ -144,7 +143,7 @@ namespace mitk
     /**
     * @brief GetData Get original data by index
     *
-    *  To ensure a mitk::Image is returned use \ref mitk::GetMitkImage
+    *  To ensure a mitk::Image is returned use GetMitkImage
     *
     * @param index
     * @return
@@ -154,7 +153,7 @@ namespace mitk
     /**
     * @brief GetData Get original data by name
     *
-    * To ensure a mitk::Image is returned use \ref mitk::GetMitkImage
+    * To ensure a mitk::Image is returned use GetMitkImage
     *
     * @param name
     * @return

Modules/ContourModel/Algorithms/mitkContourModelUtils.h

@@ -34,8 +34,11 @@ namespace mitk
     /**
       \brief Projects a contour onto an image point by point. Converts from world to index coordinates.
 
+      \param slice
+      \param contourIn3D
       \param correctionForIpSegmentation adds 0.5 to x and y index coordinates (difference between ipSegmentation and
       MITK contours)
+      \param constrainToInside
     */
     static ContourModel::Pointer ProjectContourTo2DSlice(Image *slice,
                                                          ContourModel *contourIn3D,
@@ -45,6 +48,8 @@ namespace mitk
     /**
       \brief Projects a slice index coordinates of a contour back into world coordinates.
 
+      \param sliceGeometry
+      \param contourIn2D
       \param correctionForIpSegmentation subtracts 0.5 to x and y index coordinates (difference between ipSegmentation
       and MITK contours)
     */

Modules/ContourModel/DataManagement/mitkContourModel.h

@@ -199,6 +199,7 @@ namespace mitk
 
     /** \brief Concatenate two contours.
     The starting control point of the other will be added at the end of the contour.
+    \param other
     \param timestep - the timestep at which the vertex will be add ( default 0)
     \param check - check for intersections ( default false)
     */

Modules/ContourModel/DataManagement/mitkContourModelSet.h

@@ -70,7 +70,7 @@ namespace mitk
     bool IsEmpty() const override;
 
     /** \brief Remove the given ContourModel from the container if exists.
-    \param ContourModel - the ContourModel to be removed.
+    \param contourModel - the ContourModel to be removed.
     */
     virtual bool RemoveContourModel(mitk::ContourModel *contourModel);
 

Modules/ContourModel/IO/mitkContourModelWriter.h

@@ -89,15 +89,15 @@ namespace mitk
     * Writes the geometry information of the TimeGeometry to an outstream.
     * The root tag is not included.
     * @param geometry the TimeGeometry of the contour.
-    * @param the stream to write to.
+    * @param out the stream to write to.
     */
     void WriteGeometryInformation(const mitk::TimeGeometry *geometry, std::ostream &out);
 
     /**
     * Writes the geometry information of the TimeGeometry to an outstream.
     * The root tag is not included.
     * @param geometry the TimeGeometry of the contour.
-    * @param the stream to write to.
+    * @param out the stream to write to.
     *
     * \deprecatedSince{2013_09} Please use TimeGeometry instead of TimeSlicedGeometry. For more information see
     * http://www.mitk.org/Development/Refactoring%20of%20the%20Geometry%20Classes%20-%20Part%201

Modules/Core/include/mitkAbstractFileIO.h

@@ -99,6 +99,7 @@ namespace mitk
      * If the given MIME type has nothing but its name set, the according MIME type
      * is looked up in the service registry.
      *
+     * @param baseDataType
      * @param mimeType The MIME type this reader can read.
      * @param description A human readable description of this reader.
      *

Modules/Core/include/mitkAbstractFileReader.h

@@ -85,9 +85,7 @@ namespace mitk
      * type id can be set via SetMimeType() or it will be auto-generated using \c extension,
      * having the form "application/vnd.mitk.<extension>".
      *
-     * @param extension The file extension (without a leading period) for which a registered
-     *        mime-type object is looked up and associated with this reader instance.
-     * @param description A human readable description of this reader.
+     * @param context
      */
     us::ServiceRegistration<IFileReader> RegisterService(us::ModuleContext *context = us::GetModuleContext());
     void UnregisterService();

Modules/Core/include/mitkAnnotation.h

@@ -96,9 +96,10 @@ namespace mitk
     *
     * Overwrites values in m_PropertyList only when possible (i.e. when types are compatible).
     * If you want to allow for object type changes (replacing a "visible":BoolProperty with "visible":IntProperty,
-    * set the @param replace.
+    * set \c replace.
     *
-    * @param replace true: if @param pList contains a property "visible" of type ColorProperty and our m_PropertyList
+    * @param pList
+    * @param replace true: if \c pList contains a property "visible" of type ColorProperty and our m_PropertyList
     * also has a "visible" property of a different type (e.g. BoolProperty), change the type, i.e. replace the objects
     * behind the pointer.
     *
@@ -345,8 +346,7 @@ namespace mitk
     * @brief Convenience method for setting visibility properties (instances
     * of BoolProperty)
     * @param visible If set to true, the data will be rendered. If false, the render will skip this data.
-    * @param renderer Specify a renderer if the visibility shall be specific to a renderer
-    * @param propertykey Can be used to specify a user defined name of the visibility propery.
+    * @param propertyKey Can be used to specify a user defined name of the visibility propery.
     */
     void SetVisibility(bool visible, const std::string &propertyKey = "visible");
 

Modules/Core/include/mitkApplyTransformMatrixOperation.h

@@ -24,14 +24,12 @@ namespace mitk
   class MITKCORE_EXPORT ApplyTransformMatrixOperation : public Operation
   {
   public:
-    //##Documentation
-    //##@brief Operation that applies a new vtk transform matrix.
-    //##
-    //## @param operationType is the type of the operation (see mitkOperation.h; e.g. move or add; Information for
-    // StateMachine::ExecuteOperation());
-    //## @param matrix is the vtk 4x4 vtk matrix of the transformation
-    //## @param refPoint is the reference point for realigning the plane stack
-
+    /** @brief Operation that applies a new vtk transform matrix.
+      *
+      * @param operationType is the type of the operation (see mitkOperation.h; e.g. move or add; Information for StateMachine::ExecuteOperation());
+      * @param matrix is the vtk 4x4 vtk matrix of the transformation
+      * @param refPoint is the reference point for realigning the plane stack
+      */
     ApplyTransformMatrixOperation(OperationType operationType,
                                   vtkSmartPointer<vtkMatrix4x4> matrix,
                                   mitk::Point3D refPoint);

Modules/Core/include/mitkArray.h

@@ -49,7 +49,7 @@ namespace mitk
    * @brief Copies elements of an array to this Vector
    * @param[in] array    the array whose values will be copied into the Vector. Must be of a type which overrides the []
    * operator
-   * @param return       the FixedArrray (e.g., mitk::Vector or mitk::Point) which should hold the elements of array.
+   * @return       the FixedArray (e.g., mitk::Vector or mitk::Point) which should hold the elements of array.
    * @attention array must be of dimension NVectorDimension!
    * @attention this method implicitly converts between data types.
    */

Modules/Core/include/mitkColorProperty.h

@@ -42,7 +42,7 @@ namespace mitk
    * make sure to set the mitk::RenderingModeProperty to a mode which
    * supports color (e.g. LEVELWINDOW_COLOR). For an example how to use
    * the mitk::ColorProperty see mitkImageVtkMapper2DColorTest.cpp in
-   * Core\Code\Rendering.
+   * Core/Code/Rendering.
    */
   class MITKCORE_EXPORT ColorProperty : public BaseProperty
   {

Modules/Core/include/mitkCoreServices.h

@@ -109,6 +109,7 @@ namespace mitk
     /**
      * @brief Unget a previously acquired service instance.
      * @param service The service instance to be released.
+     * @param context
      * @return \c true if ungetting the service was successful, \c false otherwise.
      */
     template <class S>

Modules/Core/include/mitkDataNode.h

@@ -202,7 +202,7 @@ namespace mitk
      *
      * Overwrites values in m_PropertyList only when possible (i.e. when types are compatible).
      * If you want to allow for object type changes (replacing a "visible":BoolProperty with "visible":IntProperty,
-     * set the \param replace.
+     * set \c replace .
      *
      * \param replace true: if \param pList contains a property "visible" of type ColorProperty and our m_PropertyList
      * also has a "visible" property of a different type (e.g. BoolProperty), change the type, i.e. replace the objects
@@ -494,7 +494,7 @@ namespace mitk
      * of BoolProperty)
      * \param visible If set to true, the data will be rendered. If false, the render will skip this data.
      * \param renderer Specify a renderer if the visibility shall be specific to a renderer
-     * \param propertykey Can be used to specify a user defined name of the visibility propery.
+     * \param propertyKey Can be used to specify a user defined name of the visibility propery.
      */
     void SetVisibility(bool visible, const mitk::BaseRenderer *renderer = nullptr, const char *propertyKey = "visible");