doxygen fixes (patch by Joachim Schleicher)

.hgignore

@@ -3,21 +3,14 @@
 ^lib$
 ^bin$
 ^build
+^doc$
 ^WinSetup$
 ^test/.*/test$
 ^test/testSuccess$
 ^config/Makefile.include$
 ^config/vigra-config$
 ^config/(aclocal.m4$|autom4te.cache)
 ^docsrc/(vigra/.*\.html|Doxyfile)$
-^doc/vigra/.*\.html$
-^doc/vigra/doxygen\.(css|gif|png)$
-^doc/vigra/(tabs|vigra)\.css$
-^doc/vigra/(tab_.|lenna_(color|gray))\.gif$
-^doc/vigra/form.*\.(gif|png)$
-^doc/vigra/formula.repository$
-^doc/vigra/classvigra_1_1.*\.(gif|png)$
-^doc/vigra/LICENSE.txt$
 ^test/multiarray/(impex/)?test[0-3]\.(tif|png)$
 ^test/impex/res\.
 ^test/impex/resrgb.gif$

config/VigraFindPackage.cmake

@@ -40,7 +40,11 @@ MACRO(VIGRA_FIND_PACKAGE package)
     foreach(path ${DEPENDENCY_SEARCH_PREFIX})
         if(NOT ${package}_FOUND)
             IF(${package} STREQUAL "Boost")
-                SET(BOOST_INCLUDEDIR ${path}/include)
+                IF(EXISTS "${path}/boost/config.hpp")
+                    SET(BOOST_INCLUDEDIR ${path}) # boost's default include path
+                ELSE()
+                    SET(BOOST_INCLUDEDIR ${path}/include) # standard include path
+                ENDIF()
                 SET(BOOST_LIBRARYDIR ${path}/lib)
             ELSE()
                 SET(CMAKE_INCLUDE_PATH ${path}/include)

docsrc/installation.dxx

@@ -19,17 +19,17 @@
 
 
     \code
-    > mkdir <vigra_build_path>       
-    > cd <vigra_build_path>       
-    > cmake [options] <vigra_source_path>
+    > mkdir \<vigra_build_path\>       
+    > cd \<vigra_build_path\>       
+    > cmake [options] \<vigra_source_path\>
     > make          # build (Linux/Unix and MinGW only)
     > make check    # compile and run tests (optional, Linux/Unix and MinGW only)
     > make doc      # generate documentation (Linux/Unix and MinGW only)
     > make install  # install (Linux/Unix and MinGW only)
     > make examples # build examples (optional, Linux/Unix and MinGW only)
     \endcode
 
-    If you use Microsoft Visual C++, you just execute cmake (not make) which creates a solution file '<vigra_build_path>/vigra.sln'. This file must be opened in Visual Studio, and the projects 'ALL_BUILD', 'check', 'doc', 'INSTALL', and 'examples' should be generated. <b>Important note</b>: If you include <b>"windows.h"</b> in your projects: there are some name clashes with VIGRA -- always include <b>"vigra/windows.h"</b> instead.
+    If you use Microsoft Visual C++, you just execute cmake (not make) which creates a solution file '&lt;vigra_build_path&gt;/vigra.sln'. This file must be opened in Visual Studio, and the projects 'ALL_BUILD', 'check', 'doc', 'INSTALL', and 'examples' should be generated. <b>Important note</b>: If you include <b>"windows.h"</b> in your projects: there are some name clashes with VIGRA -- always include <b>"vigra/windows.h"</b> instead.
 
     cmake [options] customize installation directories and guide cmake in its search for the VIGRA dependencies. On a Linux system, it is often possible to configure without any options. The most commonly used options are:
 

include/vigra/basicimage.hxx

@@ -818,11 +818,11 @@ class BasicImage
     }
 
         /** resize image to given size and initialize by copying data
-            from the C-style arra \a data.
+            from the C-style array \a data.
         */
     void resizeCopy(int width, int height, const_pointer data);
 
-        /** resize image to size of other image and copy it's data
+        /** resize image to size of other image and copy its data
         */
     void resizeCopy(const BasicImage & rhs)
     {
@@ -1090,7 +1090,7 @@ class BasicImage
 
 template <class PIXELTYPE, class Alloc>
 BasicImage<PIXELTYPE, Alloc> &
-BasicImage<PIXELTYPE, Alloc>::operator=(const BasicImage<PIXELTYPE, Alloc> & rhs)
+BasicImage<PIXELTYPE, Alloc>::operator=(const BasicImage & rhs)
 {
     if(this != &rhs)
     {
@@ -1230,7 +1230,7 @@ BasicImage<PIXELTYPE, Alloc>::resizeCopy(int width, int height, const_pointer da
 
 template <class PIXELTYPE, class Alloc>
 void
-BasicImage<PIXELTYPE, Alloc>::swap( BasicImage<PIXELTYPE, Alloc>& rhs )
+BasicImage<PIXELTYPE, Alloc>::swap( BasicImage & rhs )
 {
   if (&rhs!=this)
   {

include/vigra/bessel.hxx

@@ -265,7 +265,7 @@ void bessjyn(int n, REAL x,int &nm, double *jn, double *yn)
 
         This function wraps a number of existing implementations and falls back to 
         a rather slow algorithm if none of them is available. In particular,
-        it uses boost::math when <tt>HasBoostMath</tt> is #defined, or native 
+        it uses boost::math when <tt>HasBoostMath</tt> is \#defined, or native 
         implementations on gcc and MSVC otherwise.
 
         <b>\#include</b> \<vigra/bessel.hxx\><br>
@@ -301,7 +301,7 @@ inline double besselJ(int n, double x)
 
         This function wraps a number of existing implementations and falls back to 
         a rather slow algorithm if none of them is available. In particular,
-        it uses boost::math when <tt>HasBoostMath</tt> is #defined, or native 
+        it uses boost::math when <tt>HasBoostMath</tt> is \#defined, or native 
         implementations on gcc and MSVC otherwise.
 
         <b>\#include</b> \<vigra/bessel.hxx\><br>
@@ -334,4 +334,4 @@ inline double besselY(int n, double x)
 
 } // namespace vigra
 
-#endif // VIGRA_BESSEL_HXX
+#endif // VIGRA_BESSEL_HXX

include/vigra/localminmax.hxx

@@ -465,7 +465,7 @@ class LocalMinmaxOptions
     with the default value 1 in the destination array.
     
     The defaults can be overridden in various ways by providing 
-    \ref LocalMinmaxOptions: you can switch to the direct neighborhood
+    LocalMinmaxOptions: You can switch to the direct neighborhood
     (i.e. 4-neighborhood in 2D, 6-neighborhood in 3D, 2*N neighborhood 
     in N-D), allow minima at the border, discard minima where the function 
     value is not below a given threshold, allow extended minima
@@ -725,7 +725,7 @@ localMinima(triple<SrcIterator, SrcIterator, SrcAccessor> src,
     with the default value 1 in the destination array.
     
     The defaults can be overridden in various ways by providing 
-    \ref LocalMinmaxOptions: you can switch to the direct neighborhood
+    LocalMinmaxOptions: You can switch to the direct neighborhood
     (i.e. 4-neighborhood in 2D, 6-neighborhood in 3D, 2*N neighborhood 
     in N-D), allow maxima at the border, discard maxima where the function 
     value is not above a given threshold, allow extended maxima

include/vigra/mathutil.hxx

@@ -1069,7 +1069,7 @@ REAL legendre(unsigned int l, REAL x)
 
         Essentially calls <tt>std::sin(M_PI*x)</tt> but uses a more accurate implementation
         to make sure that <tt>sin_pi(1.0) == 0.0</tt> (which does not hold for
-        <tt>std::sin(M_PI)</tt> due to round-off error), and tt>sin_pi(0.5) == 1.0</tt>.
+        <tt>std::sin(M_PI)</tt> due to round-off error), and <tt>sin_pi(0.5) == 1.0</tt>.
 
         <b>\#include</b> \<vigra/mathutil.hxx\><br>
         Namespace: vigra
@@ -1107,7 +1107,7 @@ REAL sin_pi(REAL x)
     /*! cos(pi*x). 
 
         Essentially calls <tt>std::cos(M_PI*x)</tt> but uses a more accurate implementation
-        to make sure that <tt>cos_pi(1.0) == -1.0</tt> and tt>cos_pi(0.5) == 0.0</tt>.
+        to make sure that <tt>cos_pi(1.0) == -1.0</tt> and <tt>cos_pi(0.5) == 0.0</tt>.
 
         <b>\#include</b> \<vigra/mathutil.hxx\><br>
         Namespace: vigra

include/vigra/multi_array.hxx

@@ -1461,7 +1461,7 @@ public:
 
 template <unsigned int N, class T, class C>
 MultiArrayView<N, T, C> &
-MultiArrayView <N, T, C>::operator=(MultiArrayView<N, T, C> const & rhs)
+MultiArrayView <N, T, C>::operator=(MultiArrayView const & rhs)
 {
     if(this == &rhs)
         return *this;
@@ -2306,7 +2306,7 @@ void MultiArray <N, T, A>::reshape (const difference_type & new_shape,
 
 template <unsigned int N, class T, class A>
 inline void
-MultiArray <N, T, A>::swap (MultiArray <N, T, A> & other)
+MultiArray <N, T, A>::swap (MultiArray & other)
 {
     if (this == &other)
         return;

include/vigra/random.hxx

@@ -281,7 +281,8 @@ void RandomState<MT19937>::generateNumbers() const
     
     <b>Traits defined:</b>
     
-    <tt>FunctorTraits<RandomNumberGenerator<Engine> >::isInitializer</tt> is true (<tt>VigraTrueType</tt>).
+    \verbatim FunctorTraits<RandomNumberGenerator<Engine> >::isInitializer \endverbatim
+    is true (<tt>VigraTrueType</tt>).
 */
 template <class Engine = detail::RandomState<detail::TT800> >
 class RandomNumberGenerator
@@ -591,8 +592,10 @@ class FunctorTraits<RandomNumberGenerator<Engine> >
     
     <b>Traits defined:</b>
     
-    <tt>FunctorTraits<UniformIntRandomFunctor<Engine> >::isInitializer</tt> and
-    <tt>FunctorTraits<UniformIntRandomFunctor<Engine> >::isUnaryFunctor</tt> are true (<tt>VigraTrueType</tt>).
+    \verbatim FunctorTraits<UniformIntRandomFunctor<Engine> >::isInitializer \endverbatim
+    and
+    \verbatim FunctorTraits<UniformIntRandomFunctor<Engine> >::isUnaryFunctor \endverbatim
+    are true (<tt>VigraTrueType</tt>).
 */
 template <class Engine = RandomTT800>
 class UniformIntRandomFunctor
@@ -698,7 +701,8 @@ class FunctorTraits<UniformIntRandomFunctor<Engine> >
     
     <b>Traits defined:</b>
     
-    <tt>FunctorTraits<UniformIntRandomFunctor<Engine> >::isInitializer</tt> is true (<tt>VigraTrueType</tt>).
+    \verbatim FunctorTraits<UniformIntRandomFunctor<Engine> >::isInitializer \endverbatim
+    is true (<tt>VigraTrueType</tt>).
 */
 template <class Engine = RandomTT800>
 class UniformRandomFunctor
@@ -769,7 +773,8 @@ class FunctorTraits<UniformRandomFunctor<Engine> >
     
     <b>Traits defined:</b>
     
-    <tt>FunctorTraits<UniformIntRandomFunctor<Engine> >::isInitializer</tt> is true (<tt>VigraTrueType</tt>).
+    \verbatim FunctorTraits<UniformIntRandomFunctor<Engine> >::isInitializer \endverbatim
+    is true (<tt>VigraTrueType</tt>).
 */
 template <class Engine = RandomTT800>
 class NormalRandomFunctor

include/vigra/random_forest/rf_split.hxx

@@ -701,15 +701,17 @@ public:
         bestCurrentCounts[1].resize(ext.class_count_);
     }
     /** calculate the best gini split along a Feature Column
-     * \param column, the feature vector - has to support the [] operator
-     * \param labels, the label vector 
+     * \param column  the feature vector - has to support the [] operator
+     * \param g       ???
+     * \param labels  the label vector 
      * \param begin 
      * \param end     (in and out)
      *                begin and end iterators to the indices of the
      *                samples in the current region. 
      *                the range begin - end is sorted by the column supplied
      *                during function execution.
-     * \param class_counts
+     * \param region_response
+     *                ???
      *                class histogram of the range. 
      *
      *  precondition: begin, end valid range, 

include/vigra/random_forest/rf_visitors.hxx

@@ -186,7 +186,7 @@ class VisitorBase
      * \param tr        reference to the tree object that called this visitor
      * \param index     index in the topology_ array we currently are at
      * \param node_t    type of node we have (will be e_.... - )
-     * \param weight    Node weight of current node. 
+     * \param features  ???
      * \sa  NodeTags;
      *
      * you can create the node by using a switch on node_tag and using the 

include/vigra/rational.hxx

@@ -276,25 +276,25 @@ public:
 
             <tt>throws bad_rational</tt> if indeterminate expression.
         */
-    Rational& operator+= (const Rational& r);
+    Rational& operator+= (const Rational<IntType>& r);
 
         /** Subtract-assignment from <tt>Rational</tt>
 
             <tt>throws bad_rational</tt> if indeterminate expression.
         */
-    Rational& operator-= (const Rational& r);
+    Rational& operator-= (const Rational<IntType>& r);
 
         /** Multiply-assignment from <tt>Rational</tt>
 
             <tt>throws bad_rational</tt> if indeterminate expression.
         */
-    Rational& operator*= (const Rational& r);
+    Rational& operator*= (const Rational<IntType>& r);
 
         /** Divide-assignment from <tt>Rational</tt>
 
             <tt>throws bad_rational</tt> if indeterminate expression.
         */
-    Rational& operator/= (const Rational& r);
+    Rational& operator/= (const Rational<IntType>& r);
 
         /** Add-assignment from <tt>IntType</tt>
 

include/vigra/seededregiongrowing.hxx

@@ -161,8 +161,6 @@ struct UnlabelWatersheds
 
 } // namespace detail
 
-enum SRGType { CompleteGrow = 0, KeepContours = 1, StopAtThreshold = 2, SRGWatershedLabel = -1 };
-
 /** \addtogroup SeededRegionGrowing Region Segmentation Algorithms
     Region growing, watersheds, and voronoi tesselation
 */
@@ -174,6 +172,14 @@ enum SRGType { CompleteGrow = 0, KeepContours = 1, StopAtThreshold = 2, SRGWater
 /*                                                      */
 /********************************************************/
 
+/** Choose between different types of Region Growing */
+enum SRGType { 
+    CompleteGrow = 0, 
+    KeepContours = 1, 
+    StopAtThreshold = 2, 
+    SRGWatershedLabel = -1 
+};
+
 /** \brief Region Segmentation by means of Seeded Region Growing.
 
     This algorithm implements seeded region growing as described in

include/vigra/wigner-matrix.hxx

@@ -138,7 +138,7 @@ class WignerMatrix
           * \param theta    rotation angle
           * \param psi      rotation angle
           *
-          * \return rotated PH expansion   
+          * \retval PHresult PH expansion   
           */
     void rotatePH(NestedArray const & PH, Real phi, Real theta, Real psi,
                   NestedArray & PHresult);

test/multiarray/test.cxx

@@ -955,9 +955,10 @@ class MultiArrayNavigatorTest
 
     void testNavigator ()
     {
-        int expected[][24] = {{0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23},
-                            {0, 4, 8, 1, 5, 9, 2, 6, 10, 3, 7, 11, 12, 16, 20, 13, 17, 21, 14, 18, 22, 15, 19, 23},
-                            {0, 12, 1, 13, 2, 14, 3, 15, 4, 16, 5, 17, 6, 18, 7, 19, 8, 20, 9, 21, 10, 22, 11, 23}};
+        unsigned char expected[][24] = 
+		    {{0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23},
+            {0, 4, 8, 1, 5, 9, 2, 6, 10, 3, 7, 11, 12, 16, 20, 13, 17, 21, 14, 18, 22, 15, 19, 23},
+            {0, 12, 1, 13, 2, 14, 3, 15, 4, 16, 5, 17, 6, 18, 7, 19, 8, 20, 9, 21, 10, 22, 11, 23}};
         typedef MultiArrayNavigator<array3_type::traverser, 3> Navigator;
         for(int d=0; d<3; ++d)
         {
@@ -974,9 +975,10 @@ class MultiArrayNavigatorTest
 
     void testCoordinateNavigator ()
     {
-        int expected[][24] = {{0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23},
-                            {0, 4, 8, 1, 5, 9, 2, 6, 10, 3, 7, 11, 12, 16, 20, 13, 17, 21, 14, 18, 22, 15, 19, 23},
-                            {0, 12, 1, 13, 2, 14, 3, 15, 4, 16, 5, 17, 6, 18, 7, 19, 8, 20, 9, 21, 10, 22, 11, 23}};
+        unsigned char expected[][24] = 
+		    {{0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23},
+            {0, 4, 8, 1, 5, 9, 2, 6, 10, 3, 7, 11, 12, 16, 20, 13, 17, 21, 14, 18, 22, 15, 19, 23},
+            {0, 12, 1, 13, 2, 14, 3, 15, 4, 16, 5, 17, 6, 18, 7, 19, 8, 20, 9, 21, 10, 22, 11, 23}};
         typedef MultiCoordinateNavigator<3> Navigator;
         for(int d=0; d<3; ++d)
         {