[ADD] The libeep loader now loads the electrode positions from an ELC file of the same name

src/dataHandler/io/WLoaderBiosig.cpp

@@ -23,12 +23,10 @@
 //---------------------------------------------------------------------------
 
 #include <iostream>
-#include <fstream>
 #include <string>
 #include <vector>
-#include <boost/lexical_cast.hpp>
-#include <boost/shared_ptr.hpp>
 
+#include <boost/shared_ptr.hpp>
 
 #include "WLoaderBiosig.h"
 #include "../WEEG.h"
@@ -37,8 +35,9 @@
 #include "../../common/WLogger.h"
 #include "../../common/WStringUtils.h"
 
+
 WLoaderBiosig::WLoaderBiosig( std::string fileName )
-    : WLoader( fileName ),
+    : WLoaderEEG( fileName ),
       m_columns( 0 ),
       m_rows( 0 )
 {
@@ -70,80 +69,9 @@ void WLoaderBiosig::fillSegmentRowBased( std::vector<std::vector<double> >* segm
     }
 }
 
-WEEGElectrodeLibrary extractElectrodePositions( std::string elcFileName )
-{
-    namespace su = string_utils;
-
-    std::ifstream ifs;
-    ifs.open( elcFileName.c_str(), std::ifstream::in );
-    if( !ifs || ifs.bad() )
-    {
-        WLogger::getLogger()->addLogMessage( "Try load broken file '" + elcFileName + "'", "BiosigLoader", LL_ERROR );
-        throw std::runtime_error( "Problem during reading file. Probably file not found." );
-    }
-
-    std::string line = "";
-
-    while(  ifs.good() && line.substr( 0, 16 ) != "NumberPositions=" )  // go to number of positions
-    {
-        std::getline( ifs, line );
-        if( !ifs.good() )
-        {
-            WLogger::getLogger()->addLogMessage( "Unexpected end of file: " + elcFileName, "BiosigLoader", LL_ERROR );
-        }
-    }
-    std::vector< std::string > tokens = su::tokenize( line );
-    size_t numPositions = boost::lexical_cast< size_t >( tokens.at( 1 ) );
-
-    while( ifs.good() && line.substr( 0, 9 ) != "Positions" )  // go to line before start of positions
-    {
-        std::getline( ifs, line );
-        if( !ifs.good() )
-        {
-            WLogger::getLogger()->addLogMessage( "Unexpected end of file: " + elcFileName, "BiosigLoader", LL_ERROR );
-        }
-    }
-
-    size_t posCounter = 0;
-    WEEGElectrodeLibrary elecPos;
-    while( posCounter != numPositions && ifs.good() && line.substr( 0, 9 ) != "Labels" )  // run through all positions
-    {
-        std::getline( ifs, line );
-        if( !ifs.good() )
-        {
-            WLogger::getLogger()->addLogMessage( "Unexpected end of file: " + elcFileName, "BiosigLoader", LL_ERROR );
-        }
-        else
-        {
-            ++posCounter;
-            std::vector< std::string > lineTokens = su::tokenize( line, ":" );
-            std::string label = lineTokens.at( 0 );
-            label = su::rTrim( label );
-//                 std::cout << "Loading positions: " << label << std::endl;
-            std::vector< std::string > posTokens = su::tokenize( lineTokens.at( 1 ) );
-            double posX = boost::lexical_cast< double >( posTokens.at( 1 ) );
-            double posY = boost::lexical_cast< double >( posTokens.at( 2 ) );
-            double posZ = boost::lexical_cast< double >( posTokens.at( 3 ) );
-            wmath::WPosition pos( posX, posY, posZ );
-            elecPos.push_back( WEEGElectrodeObject( pos ) );
-//                 std::cout << "Loading positions: " << pos << std::endl;
-        }
-    }
-
-    std::getline( ifs, line );
-    assert( elecPos.size() == numPositions );
-    assert( line.substr( 0, 6 )  == "Labels" );
-
-    return elecPos;
-}
-
-
 boost::shared_ptr< WDataSet > WLoaderBiosig::load()
 {
     assert( m_fileName.substr( m_fileName.size() - 4 ) == ".edf" && "We expect only EDF so far." );
-    std::string elcFileName = m_fileName;
-    elcFileName.resize( elcFileName.size() - 3 ); // drop suffix
-    elcFileName += "elc"; // add new suffix
 
     hd =  sopen( m_fileName.c_str(), "r", 0 );
 
@@ -205,7 +133,7 @@ boost::shared_ptr< WDataSet > WLoaderBiosig::load()
     segments.push_back( segment );
 
 
-    WEEGElectrodeLibrary lib = extractElectrodePositions( elcFileName );
+    WEEGElectrodeLibrary lib = extractElectrodePositions();
 
     if( hd->NS != lib.size() )
         throw WDHException( "Contents of edf and elc files are not compatible: Different number of channels." );

src/dataHandler/io/WLoaderBiosig.h

@@ -27,17 +27,19 @@
 
 #include <string>
 #include <vector>
+
 #include <boost/shared_ptr.hpp>
 
-#include "../WLoader.h"
+#include "WLoaderEEG.h"
 #include "biosig/biosig.h"
 
+
 /**
  * Loader for several formats for biological signal.
  * Uses BiosigC++ 4.
  * \ingroup dataHandler
  */
-class WLoaderBiosig : public WLoader
+class WLoaderBiosig : public WLoaderEEG
 {
 public:
     /**

src/dataHandler/io/WLoaderEEG.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 <fstream>
+#include <string>
+#include <vector>
+
+#include <boost/lexical_cast.hpp>
+
+#include "../../common/WLogger.h"
+#include "WLoaderEEG.h"
+
+
+WLoaderEEG::WLoaderEEG( std::string fileName ) throw( WDHIOFailure )
+    : WLoader( fileName )
+{
+}
+
+WEEGElectrodeLibrary WLoaderEEG::extractElectrodePositions()
+{
+    namespace su = string_utils;
+
+    std::string elcFileName = m_fileName;
+    elcFileName.resize( elcFileName.size() - 3 ); // drop suffix
+    elcFileName += "elc"; // add new suffix
+
+    std::ifstream ifs;
+    ifs.open( elcFileName.c_str(), std::ifstream::in );
+    if( !ifs || ifs.bad() )
+    {
+        WLogger::getLogger()->addLogMessage( "Try load broken file '" + elcFileName + "'", "EEG Loader", LL_ERROR );
+        throw std::runtime_error( "Problem during reading file. Probably file not found." );
+    }
+
+    std::string line = "";
+
+    while(  ifs.good() && line.substr( 0, 16 ) != "NumberPositions=" )  // go to number of positions
+    {
+        std::getline( ifs, line );
+        if( !ifs.good() )
+        {
+            WLogger::getLogger()->addLogMessage( "Unexpected end of file: " + elcFileName, "EEG Loader", LL_ERROR );
+        }
+    }
+    std::vector< std::string > tokens = su::tokenize( line );
+    size_t numPositions = boost::lexical_cast< size_t >( tokens.at( 1 ) );
+
+    while( ifs.good() && line.substr( 0, 9 ) != "Positions" )  // go to line before start of positions
+    {
+        std::getline( ifs, line );
+        if( !ifs.good() )
+        {
+            WLogger::getLogger()->addLogMessage( "Unexpected end of file: " + elcFileName, "EEG Loader", LL_ERROR );
+        }
+    }
+
+    size_t posCounter = 0;
+    WEEGElectrodeLibrary elecPos;
+    while( posCounter != numPositions && ifs.good() && line.substr( 0, 9 ) != "Labels" )  // run through all positions
+    {
+        std::getline( ifs, line );
+        if( !ifs.good() )
+        {
+            WLogger::getLogger()->addLogMessage( "Unexpected end of file: " + elcFileName, "EEG Loader", LL_ERROR );
+        }
+        else
+        {
+            ++posCounter;
+            std::vector< std::string > lineTokens = su::tokenize( line, ":" );
+            std::string label = lineTokens.at( 0 );
+            label = su::rTrim( label );
+//                 std::cout << "Loading positions: " << label << std::endl;
+            std::vector< std::string > posTokens = su::tokenize( lineTokens.at( 1 ) );
+            double posX = boost::lexical_cast< double >( posTokens.at( 1 ) );
+            double posY = boost::lexical_cast< double >( posTokens.at( 2 ) );
+            double posZ = boost::lexical_cast< double >( posTokens.at( 3 ) );
+            wmath::WPosition pos( posX, posY, posZ );
+            elecPos.push_back( WEEGElectrodeObject( pos ) );
+//                 std::cout << "Loading positions: " << pos << std::endl;
+        }
+    }
+
+    std::getline( ifs, line );
+    assert( elecPos.size() == numPositions );
+    assert( line.substr( 0, 6 )  == "Labels" );
+
+    return elecPos;
+}

src/dataHandler/io/WLoaderEEG.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 WLOADEREEG_H
+#define WLOADEREEG_H
+
+#include <string>
+
+#include "../WEEG.h"
+#include "../WLoader.h"
+
+
+/**
+ * Abstract base class for all Loaders who handle with EEG data
+ * \ingroup dataHandler
+ */
+class WLoaderEEG : public WLoader
+{
+public:
+protected:
+    /**
+     * Constructs basic eeg Loader with a file name.
+     *
+     * \param fileName Path to be loaded
+     * \throw WDHIOFailure in case of an error
+     */
+    explicit WLoaderEEG( std::string fileName ) throw( WDHIOFailure );
+
+    /**
+     * Load electrode positions from ELC file with same name
+     *
+     * \return electrode library containig the loaded positions
+     */
+    WEEGElectrodeLibrary extractElectrodePositions();
+private:
+};
+
+#endif  // WLOADEREEG_H

src/dataHandler/io/WLoaderEEGASCII.cpp

@@ -35,8 +35,9 @@
 #include "../WSubject.h"
 #include "WLoaderEEGASCII.h"
 
+
 WLoaderEEGASCII::WLoaderEEGASCII( std::string fileName )
-    : WLoader( fileName )
+    : WLoaderEEG( fileName )
 {
 }
 
@@ -86,4 +87,3 @@ boost::shared_ptr< WDataSet > WLoaderEEGASCII::load()
     eeg->setFileName( m_fileName );
     return eeg;
 }
-

src/dataHandler/io/WLoaderEEGASCII.h

@@ -25,16 +25,18 @@
 #ifndef WLOADEREEGASCII_H
 #define WLOADEREEGASCII_H
 
-
 #include <string>
+
 #include <boost/shared_ptr.hpp>
-#include "../WLoader.h"
+
+#include "WLoaderEEG.h"
+
 
 /**
  * Loader for EEG data in ASCII fromat.
  * \ingroup dataHandler
  */
-class WLoaderEEGASCII : public WLoader
+class WLoaderEEGASCII : public WLoaderEEG
 {
 public:
     /**

src/dataHandler/io/WLoaderLibeep.cpp

@@ -36,13 +36,13 @@ extern "C"
 
 
 WLoaderLibeep::WLoaderLibeep( std::string fileName )
-    : WLoader( fileName )
+    : WLoaderEEG( fileName )
 {
 }
 
 boost::shared_ptr< WDataSet > WLoaderLibeep::load()
 {
-    WLogger::getLogger()->addLogMessage( "Opening " + m_fileName, "Libeep Loader" );
+    wlog::debug( "Libeep Loader" ) << "Opening " << m_fileName;
 
     // initialize
     FILE* file = fopen( m_fileName.c_str(), "rb" );
@@ -58,15 +58,15 @@ boost::shared_ptr< WDataSet > WLoaderLibeep::load()
     }
 
     // read data
-    int numberOfChannels = eep_get_chanc( eeg );
+    unsigned int numberOfChannels = eep_get_chanc( eeg );
     slen_t numberOfSamples = eep_get_samplec( eeg );
 
-    if( numberOfSamples > 32768 )
+    if( numberOfSamples > 8192 )
     {
         // limit maximum size of the dataset
         // TODO(cornimueller): Don't load EEG data as a whole, use blocks instead
         // TODO(wiebel): Don't load EEG data as a whole, use blocks instead
-        numberOfSamples = 32768;
+        numberOfSamples = 8192;
     }
 
     sraw_t* buffer = new sraw_t[CNTBUF_ARRAYSIZE( eeg, numberOfSamples )];
@@ -74,7 +74,7 @@ boost::shared_ptr< WDataSet > WLoaderLibeep::load()
 
     WEEGChannelLabels channelLabels( numberOfChannels );
     WEEGSegment segment( numberOfChannels );
-    for( int channel = 0; channel < numberOfChannels; ++channel )
+    for( unsigned int channel = 0; channel < numberOfChannels; ++channel )
     {
         channelLabels[channel].first = eep_get_chan_label( eeg, channel );
 
@@ -91,10 +91,17 @@ boost::shared_ptr< WDataSet > WLoaderLibeep::load()
     delete[] buffer;
     eep_fclose( eeg );
 
+    WEEGElectrodeLibrary electrodeLibrary = extractElectrodePositions();
+
+    if( electrodeLibrary.size() != numberOfChannels )
+    {
+        throw WDHException( "Contents of cnt and elc files are not compatible: Different number of channels." );
+    }
+
     // construct WEEG object and return it
     boost::shared_ptr< WEEG > out( new WEEG(
         WEEGSegmentArray( 1, segment ),
-        WEEGElectrodeLibrary( numberOfChannels, WEEGElectrodeObject( wmath::WPosition() ) ),
+        electrodeLibrary,
         channelLabels
     ) );
     out->setFileName( m_fileName );

src/dataHandler/io/WLoaderLibeep.h

@@ -27,14 +27,14 @@
 
 #include <string>
 
-#include "../WLoader.h"
+#include "WLoaderEEG.h"
 
 
 /**
  * Loader for the CNT format supported by the libeep library.
  * \ingroup dataHandler
  */
-class WLoaderLibeep : public WLoader
+class WLoaderLibeep : public WLoaderEEG
 {
 public:
     /**