[ADD #89] First versions of an abstract pager class and a pager class for CNT...

[ADD #89] First versions of an abstract pager class and a pager class for CNT files to load EEG values only on demand.

src/dataHandler/WEEGValueMatrix.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 WEEGVALUEMATRIX_H
+#define WEEGVALUEMATRIX_H
+
+#include <vector>
+
+
+/**
+ * Values of an EEG.
+ * Saved as vector of channels, and each channel is a vector of samples.
+ */
+typedef std::vector< std::vector< double > > WEEGValueMatrix;
+
+#endif  // WEEGVALUEMATRIX_H

src/dataHandler/io/WPagerEEG.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 "../../common/WIOTools.h"
+#include "../exceptions/WDHNoSuchFile.h"
+#include "WPagerEEG.h"
+
+
+WPagerEEG::~WPagerEEG()
+{
+}
+
+WPagerEEG::WPagerEEG( std::string fileName )
+    : m_fileName( fileName )
+{
+    if( !wiotools::fileExists( m_fileName ) )
+    {
+        throw WDHNoSuchFile( m_fileName + " doesn't exist" );
+    }
+}

src/dataHandler/io/WPagerEEG.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 WPAGEREEG_H
+#define WPAGEREEG_H
+
+#include <cstddef>
+
+#include <string>
+
+#include <boost/shared_ptr.hpp>
+
+#include "../WEEGValueMatrix.h"
+
+
+/**
+ * Abstract class to load an EEG file and keep it open to support paging.
+ * \ingroup dataHandler
+ */
+class WPagerEEG
+{
+public:
+    /**
+     * Virtual destructor
+     */
+    virtual ~WPagerEEG();
+
+    /**
+     * Get the values of all channels for a given sample range.
+     *
+     * \param segment segment number to read the values from
+     * \param start start sample of the sample range
+     * \param length length of the sample range
+     * \return matrix of values
+     */
+    virtual boost::shared_ptr< WEEGValueMatrix > getValues( std::size_t segment, std::size_t start, std::size_t length ) = 0;
+
+protected:
+    /**
+     * Constructor
+     *
+     * \param fileName path and filename to the file to load
+     */
+    explicit WPagerEEG( std::string fileName );
+
+    std::string m_fileName; //!< name of the loaded file
+
+private:
+};
+
+#endif  // WPAGEREEG_H

src/dataHandler/io/WPagerEEGLibeep.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 <clocale>
+#include <cstddef>
+#include <cstdio>
+
+#include <sstream>
+#include <string>
+#include <vector>
+
+#include <boost/shared_ptr.hpp>
+
+extern "C"
+{
+    #include "libeep/cnt/cnt.h"
+}
+
+#include "../../common/exceptions/WOutOfBounds.h"
+#include "../exceptions/WDHIOFailure.h"
+#include "../exceptions/WDHNoSuchFile.h"
+#include "../WEEGValueMatrix.h"
+#include "WPagerEEGLibeep.h"
+
+
+WPagerEEGLibeep::WPagerEEGLibeep( std::string fileName )
+    : WPagerEEG( fileName )
+{
+    // libeep needs the standard C locale to load float values from ASCII
+    std::setlocale( LC_NUMERIC, "C" );
+
+    // initialize
+    std::FILE* file = std::fopen( m_fileName.c_str(), "rb" );
+    if( !file )
+    {
+        throw WDHNoSuchFile( m_fileName + " could not be opened" );
+    }
+
+    int status;
+    m_eeg = eep_init_from_file( m_fileName.c_str(), file, &status );
+    if( status != CNTERR_NONE || !m_eeg )
+    {
+        std::ostringstream stream;
+        stream << m_fileName << " could not be initialized. Libeep status code: " << status;
+        throw WDHIOFailure( stream.str() );
+    }
+
+    m_nbChannels = eep_get_chanc( m_eeg );
+    m_nbSamples = eep_get_samplec( m_eeg );
+
+    m_scales = std::vector< double >( m_nbChannels );
+    for( size_t channelID = 0; channelID < m_nbChannels; ++channelID )
+    {
+        m_scales[channelID] = eep_get_chan_scale( m_eeg, channelID );
+    }
+}
+
+WPagerEEGLibeep::~WPagerEEGLibeep()
+{
+    // cleanup
+    int status = eep_fclose( m_eeg );
+    if( status != CNTERR_NONE )
+    {
+        std::ostringstream stream;
+        stream << m_fileName << " could not be closed. Libeep status code: " << status;
+        throw WDHIOFailure( stream.str() );
+    }
+}
+
+boost::shared_ptr< WEEGValueMatrix > WPagerEEGLibeep::getValues( std::size_t segment, std::size_t start, std::size_t length )
+{
+    if( segment != 0 )
+    {
+        std::ostringstream stream;
+        stream << m_fileName << " has no segment number " << segment;
+        throw WOutOfBounds( stream.str() );
+    }
+
+    if( start + length > m_nbSamples )
+    {
+        std::ostringstream stream;
+        stream << "Could not read sample number " << start + length - 1 << " of file " << m_fileName
+               << ", it has only " << m_nbSamples << " samples";
+        throw WOutOfBounds( stream.str() );
+    }
+
+    int status = eep_seek( m_eeg, DATATYPE_EEG, start, 0 );
+    if( status != CNTERR_NONE )
+    {
+        std::ostringstream stream;
+        stream << "Seek error on " << m_fileName << ". Libeep status code: " << status;
+        throw WDHIOFailure( stream.str() );
+    }
+
+    sraw_t* buffer = new sraw_t[CNTBUF_ARRAYSIZE( m_eeg, length )];
+    status = eep_read_sraw( m_eeg, DATATYPE_EEG, buffer, length );
+    if( status != CNTERR_NONE )
+    {
+        std::ostringstream stream;
+        stream << "Read error on " << m_fileName << ". Libeep status code: " << status;
+        throw WDHIOFailure( stream.str() );
+    }
+
+    boost::shared_ptr< WEEGValueMatrix > values( new WEEGValueMatrix( m_nbChannels, std::vector< double >( length ) ) );
+    for( size_t channelID = 0; channelID < m_nbChannels; ++channelID )
+    {
+        for( size_t sampleID = 0; sampleID < length; ++sampleID )
+        {
+            (*values)[channelID][sampleID] = buffer[sampleID * m_nbChannels + channelID] * m_scales[channelID];
+        }
+    }
+    delete[] buffer;
+
+    return values;
+}

src/dataHandler/io/WPagerEEGLibeep.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 WPAGEREEGLIBEEP_H
+#define WPAGEREEGLIBEEP_H
+
+#include <cstddef>
+
+#include <string>
+#include <vector>
+
+#include <boost/shared_ptr.hpp>
+
+#include "../WEEGValueMatrix.h"
+#include "WPagerEEG.h"
+
+
+/**
+ * Class to load an EEG file and keep it open to support paging.
+ * Uses the libeep library to read the CNT format.
+ * \ingroup dataHandler
+ */
+class WPagerEEGLibeep : public WPagerEEG
+{
+public:
+    /**
+     * Constructor
+     *
+     * \param fileName path and filename to a CNT file
+     */
+    explicit WPagerEEGLibeep( std::string fileName );
+
+    /**
+     * Virtual destructor
+     */
+    virtual ~WPagerEEGLibeep();
+
+    virtual boost::shared_ptr< WEEGValueMatrix > getValues( std::size_t segment, std::size_t start, std::size_t length );
+
+protected:
+private:
+    eeg_t* m_eeg; //!< handler for the cnt file opened by libeep
+
+    std::size_t m_nbChannels; //!< number of channels
+    std::size_t m_nbSamples; //!< number of samples
+
+    std::vector< double > m_scales; //!< scale factors of the channels
+};
+
+#endif  // WPAGEREEGLIBEEP_H