WMReadDipoles.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 <fstream>
#include <memory>
#include <string>
#include <vector>
 
#include "WMReadDipoles.h"
#include "core/common/WPathHelper.h"
#include "core/dataHandler/WDataSetDipoles.h"
#include "core/dataHandler/exceptions/WDHIOFailure.h"
#include "core/kernel/WKernel.h"
#include "modules/readDipoles/WMReadDipoles.xpm"
 
// This line is needed by the module loader to actually find your module. Do not remove. Do NOT add a ";" here.
W_LOADABLE_MODULE( WMReadDipoles )
 
WMReadDipoles::WMReadDipoles():
    WModule()
{
}
 
WMReadDipoles::~WMReadDipoles()
{
    // Cleanup!
}
 
std::shared_ptr< WModule > WMReadDipoles::factory() const
{
    return std::shared_ptr< WModule >( new WMReadDipoles() );
}
 
const char** WMReadDipoles::getXPMIcon() const
{
    return WMReadDipoles_xpm; // Please put a real icon here.
}
const std::string WMReadDipoles::getName() const
{
    return "Read Dipoles";
}
 
const std::string WMReadDipoles::getDescription() const
{
    return "Reading \".dip\" files containing position and additional information on dipoles reconstructed from EEG.";
}
 
void WMReadDipoles::connectors()
{
    m_dipoles = std::shared_ptr< WModuleOutputData< WDataSetDipoles > >( new WModuleOutputData< WDataSetDipoles >(
        shared_from_this(), "Dipoles", "The loaded dipoles reconstructed from EEG." ) );
    addConnector( m_dipoles );
 
    WModule::connectors();
}
 
void WMReadDipoles::properties()
{
    m_propCondition = std::shared_ptr< WCondition >( new WCondition() );
    m_dataFile = m_properties->addProperty( "File", "", WPathHelper::getAppPath(), m_propCondition );
    WPropertyHelper::PC_PATHEXISTS::addTo( m_dataFile );
 
    m_metaFile = m_properties->addProperty( "Use meta file", "File containing multiple filenames to load.", true );
 
    WModule::properties();
}
 
void WMReadDipoles::requirements()
{
    // Put the code for your requirements here. See "src/modules/template/" for an extensively documented example.
}
 
void WMReadDipoles::moduleMain()
{
    m_moduleState.add( m_propCondition );
    ready();
    while( !m_shutdownFlag() )
    {
        m_moduleState.wait();
 
        if( m_shutdownFlag() )
        {
            break;
        }
 
        std::shared_ptr< WProgress > progress( new WProgress( "Read Dipoles", 2 ) );
        ++*progress;
        if( !m_metaFile->get() )
        {
            m_dataSet = readFiles( std::vector< std::string >( 1, m_dataFile->get().string() ) );
        }
        else
        {
            m_dataSet = readMetaData( m_dataFile->get().string() );
        }
        ++*progress;
        m_dipoles->updateData( m_dataSet );
        progress->finish();
    }
}
 
 
std::shared_ptr< WDataSetDipoles > WMReadDipoles::readMetaData( std::string filename )
{
    std::vector< std::string > names;
    std::ifstream ifs;
    ifs.open( filename.c_str(), std::ifstream::in );
    if( !ifs || ifs.bad() )
    {
        throw WDHIOFailure( std::string( "Internal error while opening file" ) );
    }
    std::string line;
 
    while( std::getline( ifs, line ) )
    {
        names.push_back( line );
    }
    ifs.close();
 
    return readFiles( names );
}
 
void WMReadDipoles::readFile( std::string filename, WPosition* pos, std::vector< float >* times, std::vector< float >* magnitudes,
                              size_t* firstTimeStep, size_t* lastTimeStep )
{
    std::ifstream ifs;
    ifs.open( filename.c_str(), std::ifstream::in );
    if( !ifs || ifs.bad() )
    {
        throw WDHIOFailure( std::string( "Internal error while opening file" ) );
    }
 
    std::string line;
    std::vector< std::string > tokens;
 
    std::getline( ifs, line, '\n' );
 
    while( line.find( "NumberTimeSteps" ) )
    {
       std::getline( ifs, line, '\n' );
    }
    tokens = string_utils::tokenize( line );
    size_t nbTimeSteps = string_utils::fromString< size_t >( tokens[1].c_str() );
 
    std::getline( ifs, line, '\n' );
 
    while( line.find( "TimeSteps" ) )
    {
       std::getline( ifs, line, '\n' );
    }
    tokens = string_utils::tokenize( line );
    tokens = string_utils::tokenize( tokens[1], "()" );
    float timeFirst = string_utils::fromString< float >( tokens[0].c_str() );
    float timeDistance = string_utils::fromString< float >( tokens[1].c_str() );
    float timeLast = string_utils::fromString< float >( tokens[2].c_str() );
    times->resize( nbTimeSteps );
    for( size_t timeStep = 0; timeStep < nbTimeSteps; ++timeStep )
    {
        (*times)[timeStep] = timeFirst + timeStep * timeDistance;
    }
    WAssert( std::abs( (*times)[nbTimeSteps-1] - timeLast ) < 1e-4, "Error during filling times vector." );
 
    while( line.find( "FirstTimeStep" ) )
    {
       std::getline( ifs, line, '\n' );
    }
    tokens = string_utils::tokenize( line );
    *firstTimeStep = std::max( string_utils::fromString< size_t >( tokens[1].c_str() ) - 1u, size_t( 0u ) );
 
    while( line.find( "LastTimeStep" ) )
    {
       std::getline( ifs, line, '\n' );
    }
    tokens = string_utils::tokenize( line );
    *lastTimeStep = std::min( string_utils::fromString< size_t >( tokens[1].c_str() ) + 1u, nbTimeSteps - 1u );
 
    while( line.find( "PositionsFixed" ) )
    {
       std::getline( ifs, line, '\n' );
    }
 
    ifs >> (*pos)[0] >> (*pos)[1] >> (*pos)[2];
 
    while( line.find( "Magnitudes" ) )
    {
       std::getline( ifs, line, '\n' );
    }
    std::getline( ifs, line, '\n' );
 
    magnitudes->clear();
    tokens = string_utils::tokenize( line );
    for( unsigned int tokenId = 0; tokenId < tokens.size(); ++tokenId )
    {
        magnitudes->push_back( string_utils::fromString< float >( tokens[tokenId].c_str() ) );
    }
 
    WAssert( magnitudes->size() == nbTimeSteps, "Number of time steps and magnitudes must be equal" );
    WAssert( times->size() == nbTimeSteps, "Number of time steps and times must be equal" );
 
    ifs.close();
}
 
std::shared_ptr< WDataSetDipoles > WMReadDipoles::readFiles( std::vector< std::string > filenames )
{
    WPosition pos;
    std::vector< float > times;
    std::vector< float > magnitudes;
    size_t firstTimeStep;
    size_t lastTimeStep;
 
    readFile( filenames[0], &pos, &times, &magnitudes, &firstTimeStep, &lastTimeStep );
    std::shared_ptr< WDataSetDipoles > loadedData( new WDataSetDipoles( pos, magnitudes, times, firstTimeStep, lastTimeStep ) );
 
    for( size_t fileId = 1; fileId < filenames.size(); ++fileId )
    {
        readFile( filenames[fileId], &pos, &times, &magnitudes, &firstTimeStep, &lastTimeStep );
        loadedData->addDipole( pos, magnitudes, times, firstTimeStep, lastTimeStep );
    }
 
    return loadedData;
}