[ADD #157] Saving of DLtLookUpTable now possible

src/dataHandler/io/WWriter.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 <string>
+
+#include "WWriter.h"
+#include "WIOTools.hpp"
+#include "../exceptions/WDHIOFailure.h"
+
+WWriter::WWriter( std::string fname, bool overwrite )
+    : m_overwrite( overwrite )
+{
+    setFileName( fname ); // not in constructor list since fileExcsits check
+}
+
+void WWriter::setFileName( std::string fname )
+{
+    m_fname = fname;
+    if( !m_overwrite && wiotools::fileExists( m_fname ) )
+    {
+        throw WDHIOFailure( "File '" + m_fname + "' already exists, skip writing" );
+    }
+}

src/dataHandler/io/WWriter.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 WWRITER_H
+#define WWRITER_H
+
+#include <string>
+
+/**
+ * Writes some data to a file. This class is only for convenience access to
+ * rudimentary file management things such as: file exists, if the given
+ * file should be overwritten, etc. Subclasses may use those mechanisms in
+ * their own public memberfunctions where the signature is different every
+ * time. e.g. writeFibs( WDataSetFibers ds );
+ */
+class WWriter
+{
+public:
+    /**
+     * Creates a writer object for writing something to a file. Use the flags
+     * to specify the behaviour.
+     *
+     * \param fname path to the target file where stuff will be written to
+     * \param overwrite If true existing files will be overwritten
+     */
+    WWriter( std::string fname, bool overwrite = false );
+
+    /**
+     * Reset the destination (file) where the writing should take place.
+     */
+    void setFileName( std::string fname );
+
+protected:
+    std::string m_fname; //!< Absolute path of the file to write to
+    bool m_overwrite; //!< flag indicating if the file may be overwritten (true) or not (false)
+
+private:
+};
+
+#endif  // WWRITER_H

src/dataHandler/io/WWriterVTK.cpp → src/dataHandler/io/WWriterFiberVTK.cpp

@@ -28,27 +28,17 @@
 
 #include <boost/shared_ptr.hpp>
 
-#include "WWriterVTK.h"
+#include "WWriterFiberVTK.h"
 #include "WIOTools.hpp"
 #include "../WDataSetFibers.h"
 #include "../exceptions/WDHIOFailure.h"
 
-WWriterVTK::WWriterVTK( std::string fname, bool overwrite )
-    : m_overwrite( overwrite )
+WWriterFiberVTK::WWriterFiberVTK( std::string fname, bool overwrite )
+    : WWriter( fname, overwrite )
 {
-    setFileName( fname );
 }
 
-void WWriterVTK::setFileName( std::string fname )
-{
-    m_fname = fname;
-    if( !m_overwrite && wiotools::fileExists( m_fname ) )
-    {
-        throw WDHIOFailure( "File '" + m_fname + "' already exists, skip writing" );
-    }
-}
-
-void WWriterVTK::writeFibs( boost::shared_ptr< const WDataSetFibers > fiberDS ) const
+void WWriterFiberVTK::writeFibs( boost::shared_ptr< const WDataSetFibers > fiberDS ) const
 {
     using std::fstream;
     fstream out( m_fname.c_str(), fstream::out | fstream::in | fstream::trunc );
@@ -56,7 +46,7 @@ void WWriterVTK::writeFibs( boost::shared_ptr< const WDataSetFibers > fiberDS )
     {
         throw WDHIOFailure( "Invalid file, or permission: " + m_fname );
     }
-    out << "# vtk DataFile Version 3.0" << std::endl;
+    out << "# VTK DataFile Version 3.0" << std::endl;
     out << "Fibers from OpenWalnut" << std::endl;
     out << "BINARY" << std::endl;
     out << "DATASET POLYDATA" << std::endl;

src/dataHandler/io/WWriterVTK.h → src/dataHandler/io/WWriterFiberVTK.h

@@ -22,32 +22,27 @@
 //
 //---------------------------------------------------------------------------
 
-#ifndef WWRITERVTK_H
-#define WWRITERVTK_H
+#ifndef WWRITERFIBERVTK_H
+#define WWRITERFIBERVTK_H
 
 #include <string>
 
 #include <boost/shared_ptr.hpp>
 
 #include "../WDataSetFibers.h"
+#include "WWriter.h"
 
 /**
- * Writes a VTK file.
+ * Writes a FiberVTK file.
  */
-class WWriterVTK
+class WWriterFiberVTK : public WWriter
 {
 public:
     /**
-     * Creates a writer object for VTK file writing.
-     *
-     * \param fname absolute file name
+     * Creates a writer object for FiberVTK file writing. On parameter documentation
+     * take a look into the WWriter class.
      */
-    explicit WWriterVTK( std::string fname, bool overwrite = false );
-
-    /**
-     * Reset the destination (file) where the writing should take place.
-     */
-    void setFileName( std::string fname );
+    WWriterFiberVTK( std::string fname, bool overwrite = false );
 
     /**
      * Writes a WDataSetFibers down to the previousely given file
@@ -55,10 +50,7 @@ public:
     void writeFibs( boost::shared_ptr< const WDataSetFibers > fiberDS ) const;
 
 protected:
-
 private:
-    std::string m_fname; //!< Absolute path of the file to write to
-    bool m_overwrite; //!< flag indicating if the file may be overwritten (true) or not (false)
 };
 
-#endif  // WWRITERVTK_H
+#endif  // WWRITERFIBERVTK_H

src/dataHandler/io/WWriterLookUpTableVTK.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 <cassert>
+#include <fstream>
+#include <string>
+#include <vector>
+
+#include <boost/shared_ptr.hpp>
+
+#include "WWriterLookUpTableVTK.h"
+#include "WIOTools.hpp"
+#include "../exceptions/WDHIOFailure.h"
+
+WWriterLookUpTableVTK::WWriterLookUpTableVTK( std::string fname, bool overwrite )
+    : WWriter( fname, overwrite )
+{
+}
+
+void WWriterLookUpTableVTK::writeTable( const std::vector< double > &table ) const
+{
+    using std::fstream;
+    fstream out( m_fname.c_str(), fstream::out | fstream::in | fstream::trunc );
+    if( !out || out.bad() )
+    {
+        throw WDHIOFailure( "Invalid file, or permission: " + m_fname );
+    }
+    out << "# vtk DataFile Version 3.0" << std::endl;
+    out << "DXtLookUpTable from OpenWalnut" << std::endl;
+    out << "BINARY" << std::endl;
+
+    out << "FIELD DXtLookUpTable 1" << std::endl;
+    unsigned int numDistances = table.size();
+    out << "DISTANCES " << numDistances << " 1 float" << std::endl;
+    float *data = new float[numDistances];
+
+    for( size_t i = 0; i < numDistances; ++i )
+    {
+        data[i] = static_cast< float >( table[i] );
+    }
+
+    wiotools::switchByteOrderOfArray< float >( data, numDistances );
+    out.write( reinterpret_cast< char* >( data ), sizeof( float ) * numDistances );
+    out << std::endl;
+    out.close();
+}

src/dataHandler/io/WWriterLookUpTableVTK.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 WWRITERLOOKUPTABLEVTK_H
+#define WWRITERLOOKUPTABLEVTK_H
+
+#include <string>
+#include <vector>
+
+#include <boost/shared_ptr.hpp>
+
+#include "WWriter.h"
+
+/**
+ * Can write a look up table to a file in VTK format.
+ */
+class WWriterLookUpTableVTK : public WWriter
+{
+public:
+    /**
+     * Creates a writer object for FiberVTK file writing. On parameter documentation
+     * take a look into the WWriter class.
+     */
+    WWriterLookUpTableVTK( std::string fname, bool overwrite = false );
+
+    /**
+     * Actually perform writing to file.
+     *
+     * \param table The data in that table will be saved
+     * \param dim the dimensionality of the table
+     */
+    void writeTable( const std::vector< double > &table ) const;
+
+protected:
+private:
+};
+
+#endif  // WWRITERLOOKUPTABLEVTK_H

src/modules/fiberClustering/WDXtLookUpTable.cpp

@@ -24,6 +24,7 @@
 
 #include <cassert>
 #include <algorithm>
+#include <vector>
 
 #include "WDXtLookUpTable.h"
 
@@ -42,3 +43,18 @@ double& WDXtLookUpTable::operator()( size_t i, size_t j )
     }
     return _data.at( i * _dim + j - ( i + 1 ) * ( i + 2 ) / 2 );
 }
+
+size_t WDXtLookUpTable::size() const
+{
+    return _data.size();
+}
+
+size_t WDXtLookUpTable::dim() const
+{
+    return _dim;
+}
+
+const std::vector< double >& WDXtLookUpTable::getData() const
+{
+    return _data;
+}

src/modules/fiberClustering/WDXtLookUpTable.h

@@ -52,9 +52,25 @@ public:
      */
     double& operator()( size_t i, size_t j );
 
+    /**
+     * \return the number of distances inside this table.
+     */
+    size_t size() const;
+
+    /**
+     * \return the dimensionality of this table
+     */
+    size_t dim() const;
+
+    /**
+     * \return readonly access to the internal data
+     */
+    const std::vector< double >& getData() const;
+
 private:
     /**
-     * Internal data structure to store the elements.
+     * Internal data structure to store the elements. The order is line major
+     * meaning first element (0,0)...(0,n-1),(1,0)...(1, n-1)...
      */
     std::vector< double > _data;
 

src/modules/fiberClustering/WMFiberClustering.cpp

@@ -42,6 +42,7 @@
 #include "../../dataHandler/WDataHandler.h"
 #include "../../dataHandler/WSubject.h"
 #include "../../dataHandler/WDataSetFibers.h"
+#include "../../dataHandler/io/WWriterLookUpTableVTK.h"
 #include "../../kernel/WKernel.h"
 #include "../../utils/WColorUtils.h"
 
@@ -195,6 +196,8 @@ void WMFiberClustering::cluster()
     std::cout << "Using " << m_clusters.size() << " clusters.";
 
     m_lastFibsSize = m_fibs->size();
+    WWriterLookUpTableVTK w( "/tmp/pansen.dist", true );
+    w.writeTable( m_dLtTable->getData() );
 }
 
 osg::ref_ptr< osg::Geode > WMFiberClustering::genFiberGeode( const WFiberCluster &cluster, const WColor color ) const

src/modules/fiberCulling/WMFiberCulling.cpp

@@ -39,7 +39,7 @@
 #include "../../dataHandler/WDataHandler.h"
 #include "../../dataHandler/WSubject.h"
 #include "../../dataHandler/WDataSetFibers.h"
-#include "../../dataHandler/io/WWriterVTK.h"
+#include "../../dataHandler/io/WWriterFiberVTK.h"
 #include "../../kernel/WKernel.h"
 #include "../../utils/WColorUtils.h"
 
@@ -143,10 +143,8 @@ void WMFiberCulling::cullOutFibers( boost::shared_ptr< WDataSetFibers > fibers )
     std::cout << "Erasing done." << std::endl;
     std::cout << "Culled out " << numFibers - fibers->size() << " fibers" << std::endl;
     std::cout << "There are " << fibers->size() << " fibers left." << std::endl;
-    if( true )
-    {
-        WWriterVTK w( "/tmp/pansen", true );
-        w.writeFibs( fibers );
-//        std::cout << "Saved fibers left from culling to " <<  << " done." << std::endl;
-    }
+
+    // TODO(math): make saving parameter dependent, and apply the desired path for saving
+    WWriterFiberVTK w( "/tmp/pansen.fib", true );
+    w.writeFibs( fibers );
 }