[CHANGE #157] Changed the metric infrastructure, so we may now easy use other...

[CHANGE #157] Changed the metric infrastructure, so we may now easy use other fiber similarity metrics.

src/math/CMakeLists.txt

+ADD_SUBDIRECTORY( fiberSimilarity )
+
 FILE( GLOB MATH_SRC "*.[c,h]pp" )
+FILE( GLOB FIBERSIMILARITY_SRC "fiberSimilarity/*.[c,h]pp" )
 
-ADD_LIBRARY( math SHARED ${MATH_SRC} )
+ADD_LIBRARY( math SHARED ${MATH_SRC} ${FIBERSIMILARITY_SRC} )
 
 # Unit tests
 IF( CXXTEST_FOUND )

src/math/WFiber.cpp

@@ -22,12 +22,9 @@
 //
 //---------------------------------------------------------------------------
 
-#include <algorithm>
-#include <utility>
 #include <vector>
 
 #include "WFiber.h"
-#include "../common/WLimits.h"
 
 namespace wmath
 {
@@ -35,63 +32,4 @@ namespace wmath
         : WLine( points )
     {
     }
-
-    std::pair< double, double > WFiber::dXt_optimized( const WFiber &other,
-                                                       const double thresholdSquare ) const
-    {
-        const WFiber &q = *this;
-        const WFiber &r = other;
-        const size_t qsize = q.size();
-        const size_t rsize = r.size();
-        double qr = 0.0;
-        double rq = 0.0;
-
-        std::vector< std::vector< double > > m( qsize, std::vector< double >( rsize, 0.0 ) );
-        for( size_t i = 0; i < qsize; ++i )
-        {
-            for( size_t j = 0; j < rsize; ++j )
-            {
-                m[i][j] = q[i].distanceSquare( r[j] );
-            }
-        }
-        double minSoFar;
-        for( size_t i = 0; i < qsize; ++i )
-        {
-            minSoFar = *( std::min_element( m[i].begin(), m[i].end() ) );
-            if( minSoFar > thresholdSquare )
-            {
-                qr += sqrt( minSoFar );
-            }
-        }
-        qr = qr / qsize;
-        for( size_t j = 0; j < rsize; ++j )
-        {
-            minSoFar = wlimits::MAX_DOUBLE;
-            for( size_t i = 0; i < qsize; ++i )
-            {
-                if( m[i][j] < minSoFar )
-                {
-                    minSoFar = m[i][j];
-                }
-            }
-            if( minSoFar > thresholdSquare )
-            {
-                rq += sqrt( minSoFar );
-            }
-        }
-        rq = rq / rsize;
-        return std::make_pair( qr, rq );
-    }
-
-    double WFiber::dSt( const WFiber& other, const double thresholdSquare ) const
-    {
-        std::pair< double, double > result = dXt_optimized( other, thresholdSquare );
-        return std::min( result.first, result.second );
-    }
-
-    double WFiber::dLt( const WFiber& other, const double thresholdSquare ) const
-    {
-        std::pair< double, double > result = dXt_optimized( other, thresholdSquare );
-        return std::max( result.first, result.second );
-    }
 }

src/math/WFiber.h

@@ -46,46 +46,6 @@ friend class WFiberTest;
 public:
     explicit WFiber( const std::vector< WPosition > &points );
 
-    /**
-     * Optimized version which computes dt measure from fibers Q and R.
-     * Since this is not symmetric it computes both: dt(Q,R) and dt(R,Q) at
-     * once. dt(Q,R) computes the mean euclidian distance of the closest
-     * points. See Paper from Zhang: doi.ieeecomputersociety.org/10.1109/TVCG.2008.52
-     *
-     * \param other The other fiber R
-     * \param thresholdSquare The threshold, where distances below will be
-     * ignored for dt() computation. Note that this parameter is given
-     * as square, since the distanceSquare is much faster to compute then
-     * just the distance.
-     * \return Both dt(Q,R) and dt(R,Q).
-     */
-    std::pair< double, double > dXt_optimized( const WFiber &other,
-                                               const double thresholdSquare ) const;
-
-    /**
-     * Computes dt(Q, R, t) and dt(R, Q, t) and then the one which is smaller
-     * is returned. Note this distance metric is symmetric.
-     *
-     * \param other The other fiber "R", while this fiber is taken as "Q".
-     * \param thresholdSquare The threshold upto which the accumulated
-     * distances should be considered
-     *
-     * \return The minimum of dt(Q, R, t) and dt(R, Q, t)
-     */
-    double dSt( const WFiber &other, const double thresholdSquare = 0.0 ) const;
-
-    /**
-     * Computes dt(Q, R, t) and dt(R, Q, t) and then the one which is smaller
-     * is returned. Note this distance metric is symmetric.
-     *
-     * \param other The other fiber "R", while this fiber is taken as "Q".
-     * \param thresholdSquare The threshold upto which the accumulated
-     * distances should be considered
-     *
-     * \return The maximum dt(Q, R, t) and dt(R, Q, t)
-     */
-    double dLt( const WFiber &other, const double thresholdSquare = 0.0 ) const;
-
 protected:
 private:
 };

src/math/fiberSimilarity/CMakeLists.txt

+FILE( GLOB FIBERSIMILARITY_SRC "*.[c,h]pp" )
+
+# Unit tests
+IF( CXXTEST_FOUND )
+  CXXTEST_ADD_TESTS_FROM_LIST( "${FIBERSIMILARITY_SRC}" 
+                               "math;common" 
+                               "WFiberSimilarity.cpp" # This is just an interface
+                              )
+ENDIF( CXXTEST_FOUND )

src/math/fiberSimilarity/WDLTMetric.cpp

+//---------------------------------------------------------------------------
+//
+// Project: OpenWalnut ( http://www.openwalnut.org )
+//
+// Copyright 2009 OpenWalnut Community, BSV@Uni-Leipzig and CNCF@MPI-CBS
+// For more information see http://www.openwalnut.org/copying
+//
+// This file is part of OpenWalnut.
+//
+// OpenWalnut is free software: you can redistribute it and/or modify
+// it under the terms of the GNU Lesser General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// OpenWalnut is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with OpenWalnut. If not, see <http://www.gnu.org/licenses/>.
+//
+//---------------------------------------------------------------------------
+
+#include <algorithm>
+#include <utility>
+
+#include "WDLTMetric.h"
+
+WDLTMetric::WDLTMetric( double thresholdSquare )
+    : WZhangMetric( thresholdSquare )
+{
+}
+
+double WDLTMetric::dist( const wmath::WFiber &q, const wmath::WFiber &r ) const
+{
+    std::pair< double, double > result = dXt_optimized( q, r );
+    return std::max( result.first, result.second );
+}

src/math/fiberSimilarity/WDLTMetric.h

+//---------------------------------------------------------------------------
+//
+// Project: OpenWalnut ( http://www.openwalnut.org )
+//
+// Copyright 2009 OpenWalnut Community, BSV@Uni-Leipzig and CNCF@MPI-CBS
+// For more information see http://www.openwalnut.org/copying
+//
+// This file is part of OpenWalnut.
+//
+// OpenWalnut is free software: you can redistribute it and/or modify
+// it under the terms of the GNU Lesser General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// OpenWalnut is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with OpenWalnut. If not, see <http://www.gnu.org/licenses/>.
+//
+//---------------------------------------------------------------------------
+
+#ifndef WDLTMETRIC_H
+#define WDLTMETRIC_H
+
+#include "WZhangMetric.h"
+#include "../WFiber.h"
+
+/**
+ * This is the Larger thresholded distance as described by Zhang.
+ */
+class WDLTMetric : public WZhangMetric
+{
+public:
+    /**
+     * Constructs this metric with a certain threshold.
+     */
+    explicit WDLTMetric( double thresholdSquare );
+
+    /**
+     * \return The maximum of dt(Q,R) and dt(R,Q)
+     */
+    virtual double dist( const wmath::WFiber &q, const wmath::WFiber &r ) const;
+
+private:
+};
+
+#endif  // WDLTMETRIC_H

src/math/fiberSimilarity/WDSTMetric.cpp

+//---------------------------------------------------------------------------
+//
+// Project: OpenWalnut ( http://www.openwalnut.org )
+//
+// Copyright 2009 OpenWalnut Community, BSV@Uni-Leipzig and CNCF@MPI-CBS
+// For more information see http://www.openwalnut.org/copying
+//
+// This file is part of OpenWalnut.
+//
+// OpenWalnut is free software: you can redistribute it and/or modify
+// it under the terms of the GNU Lesser General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// OpenWalnut is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with OpenWalnut. If not, see <http://www.gnu.org/licenses/>.
+//
+//---------------------------------------------------------------------------
+
+#include <algorithm>
+#include <utility>
+
+#include "WDSTMetric.h"
+
+WDSTMetric::WDSTMetric( double thresholdSquare )
+    : WZhangMetric( thresholdSquare )
+{
+}
+
+double WDSTMetric::dist( const wmath::WFiber &q, const wmath::WFiber &r ) const
+{
+    std::pair< double, double > result = dXt_optimized( q, r );
+    return std::min( result.first, result.second );
+}
+

src/math/fiberSimilarity/WDSTMetric.h

+//---------------------------------------------------------------------------
+//
+// Project: OpenWalnut ( http://www.openwalnut.org )
+//
+// Copyright 2009 OpenWalnut Community, BSV@Uni-Leipzig and CNCF@MPI-CBS
+// For more information see http://www.openwalnut.org/copying
+//
+// This file is part of OpenWalnut.
+//
+// OpenWalnut is free software: you can redistribute it and/or modify
+// it under the terms of the GNU Lesser General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// OpenWalnut is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with OpenWalnut. If not, see <http://www.gnu.org/licenses/>.
+//
+//---------------------------------------------------------------------------
+
+#ifndef WDSTMETRIC_H
+#define WDSTMETRIC_H
+
+#include "WZhangMetric.h"
+#include "../WFiber.h"
+
+/**
+ * This is the Smaller thresholded distance as described by Zhang.
+ */
+class WDSTMetric : WZhangMetric
+{
+public:
+    /**
+     * Constructs this metric with a certain threshold.
+     */
+    explicit WDSTMetric( double thresholdSquare );
+
+    /**
+     * \return The minimum of dt(Q, R, t) and dt(R, Q, t)
+     */
+    virtual double dist( const wmath::WFiber &q, const wmath::WFiber &ri ) const;
+
+private:
+};
+
+#endif  // WDSTMETRIC_H

src/math/fiberSimilarity/WFiberSimilarity.cpp

+//---------------------------------------------------------------------------
+//
+// Project: OpenWalnut ( http://www.openwalnut.org )
+//
+// Copyright 2009 OpenWalnut Community, BSV@Uni-Leipzig and CNCF@MPI-CBS
+// For more information see http://www.openwalnut.org/copying
+//
+// This file is part of OpenWalnut.
+//
+// OpenWalnut is free software: you can redistribute it and/or modify
+// it under the terms of the GNU Lesser General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// OpenWalnut is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with OpenWalnut. If not, see <http://www.gnu.org/licenses/>.
+//
+//---------------------------------------------------------------------------
+
+#include "WFiberSimilarity.h"
+
+WFiberSimilarity::~WFiberSimilarity()
+{
+}

src/math/fiberSimilarity/WFiberSimilarity.h

+//---------------------------------------------------------------------------
+//
+// Project: OpenWalnut ( http://www.openwalnut.org )
+//
+// Copyright 2009 OpenWalnut Community, BSV@Uni-Leipzig and CNCF@MPI-CBS
+// For more information see http://www.openwalnut.org/copying
+//
+// This file is part of OpenWalnut.
+//
+// OpenWalnut is free software: you can redistribute it and/or modify
+// it under the terms of the GNU Lesser General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// OpenWalnut is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with OpenWalnut. If not, see <http://www.gnu.org/licenses/>.
+//
+//---------------------------------------------------------------------------
+
+#ifndef WFIBERSIMILARITY_H
+#define WFIBERSIMILARITY_H
+
+namespace wmath
+{
+    class WFiber;
+}
+
+/**
+ * Abstract interface to all fiber similarity measures. The term
+ * "fiber-similarity" is closely related to the term fiber-distance. Basically
+ * fibers that are very close to each other (low distance) are considered
+ * similar.
+ */
+class WFiberSimilarity
+{
+public:
+    /**
+     * Computes the similarity between two fibers Q and R. Values near 0
+     * indicate very strong similarity and low distance.
+     */
+    virtual double dist( const wmath::WFiber &q, const wmath::WFiber &r ) const = 0;
+
+    /**
+     * Virtual destructor since there is a virtual member function.
+     */
+    virtual ~WFiberSimilarity();
+
+protected:
+private:
+};
+
+#endif  // WFIBERSIMILARITY_H

src/math/fiberSimilarity/WZhangMetric.cpp

+//---------------------------------------------------------------------------
+//
+// Project: OpenWalnut ( http://www.openwalnut.org )
+//
+// Copyright 2009 OpenWalnut Community, BSV@Uni-Leipzig and CNCF@MPI-CBS
+// For more information see http://www.openwalnut.org/copying
+//
+// This file is part of OpenWalnut.
+//
+// OpenWalnut is free software: you can redistribute it and/or modify
+// it under the terms of the GNU Lesser General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// OpenWalnut is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with OpenWalnut. If not, see <http://www.gnu.org/licenses/>.
+//
+//---------------------------------------------------------------------------
+
+#include <algorithm>
+#include <utility>
+#include <vector>
+
+#include "WZhangMetric.h"
+#include "../../common/WLimits.h"
+
+WZhangMetric::WZhangMetric( double thresholdSquare )
+    : m_thresholdSquare( thresholdSquare )
+{
+}
+
+void WZhangMetric::setThreshold( double thresholdSquare )
+{
+    m_thresholdSquare = thresholdSquare;
+}
+
+std::pair< double, double > WZhangMetric::dXt_optimized( const wmath::WFiber &q,
+        const wmath::WFiber &r ) const
+{
+    const size_t qsize = q.size();
+    const size_t rsize = r.size();
+    double qr = 0.0;
+    double rq = 0.0;
+
+    // will contain every point-to-point square-distances
+    std::vector< std::vector< double > > m( qsize, std::vector< double >( rsize, 0.0 ) );
+    for( size_t i = 0; i < qsize; ++i )
+    {
+        for( size_t j = 0; j < rsize; ++j )
+        {
+            m[i][j] = q[i].distanceSquare( r[j] );
+        }
+    }
+    // compute dt(q,r)
+    double minSoFar;
+    for( size_t i = 0; i < qsize; ++i )
+    {
+        minSoFar = *( std::min_element( m[i].begin(), m[i].end() ) );
+        if( minSoFar > m_thresholdSquare )
+        {
+            qr += sqrt( minSoFar );
+        }
+    }
+    qr = qr / qsize;
+    // compute dt(r,q)
+    for( size_t j = 0; j < rsize; ++j )
+    {
+        minSoFar = wlimits::MAX_DOUBLE;
+        for( size_t i = 0; i < qsize; ++i )
+        {
+            if( m[i][j] < minSoFar )
+            {
+                minSoFar = m[i][j];
+            }
+        }
+        if( minSoFar > m_thresholdSquare )
+        {
+            rq += sqrt( minSoFar );
+        }
+    }
+    rq = rq / rsize;
+    return std::make_pair( qr, rq );
+}
+
+
+

src/math/fiberSimilarity/WZhangMetric.h

+//---------------------------------------------------------------------------
+//
+// Project: OpenWalnut ( http://www.openwalnut.org )
+//
+// Copyright 2009 OpenWalnut Community, BSV@Uni-Leipzig and CNCF@MPI-CBS
+// For more information see http://www.openwalnut.org/copying
+//
+// This file is part of OpenWalnut.
+//
+// OpenWalnut is free software: you can redistribute it and/or modify
+// it under the terms of the GNU Lesser General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// OpenWalnut is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with OpenWalnut. If not, see <http://www.gnu.org/licenses/>.
+//
+//---------------------------------------------------------------------------
+
+#ifndef WZHANGMETRIC_H
+#define WZHANGMETRIC_H
+
+#include <utility>
+
+#include "WFiberSimilarity.h"
+#include "../WFiber.h"
+
+/**
+ * Abstract class which prepares the implementation of the thresholded mean min
+ * distance as introduced by Zhang etal: http://dx.doi.org/10.1109/TVCG.2008.52
+ */
+class WZhangMetric : public WFiberSimilarity
+{
+public:
+    /**
+     * Constructs new algorithm with its threshold for minimal square
+     * distances.
+     */
+    explicit WZhangMetric( double thresholdSquare );
+
+    /**
+     * Resets the threshold for minimal point distances used in computation.
+     */
+    void setThreshold( double thresholdSquare );
+
+protected:
+    /**
+     * Optimized version which computes dt measure from fibers Q and R.
+     * Since this is not symmetric it computes both: dt(Q,R) and dt(R,Q) at
+     * once. dt(Q,R) computes the mean euclidian distance of the closest
+     * points.
+     *
+     * \param q The first fiber
+     * \param r The second fiber
+     * \return Both dt(Q,R) and dt(R,Q).
+     */
+    std::pair< double, double > dXt_optimized( const wmath::WFiber &q, const wmath::WFiber &r ) const;
+
+private:
+    /**
+     * Threshold upto this point-distances are threaded as zero-distance.
+     */
+    double m_thresholdSquare;
+};
+
+#endif  // WZHANGMETRIC_H

src/math/fiberSimilarity/test/WDLTMetric_test.h

+//---------------------------------------------------------------------------
+//
+// Project: OpenWalnut ( http://www.openwalnut.org )
+//
+// Copyright 2009 OpenWalnut Community, BSV@Uni-Leipzig and CNCF@MPI-CBS
+// For more information see http://www.openwalnut.org/copying
+//
+// This file is part of OpenWalnut.
+//
+// OpenWalnut is free software: you can redistribute it and/or modify
+// it under the terms of the GNU Lesser General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// OpenWalnut is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with OpenWalnut. If not, see <http://www.gnu.org/licenses/>.
+//
+//---------------------------------------------------------------------------
+
+#ifndef WDLTMETRIC_TEST_H
+#define WDLTMETRIC_TEST_H
+
+#include <vector>
+
+#include <cxxtest/TestSuite.h>
+
+#include "../WDLTMetric.h"