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|
//---------------------------------------------------------------------------
//
// 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 <vector>
#include "core/common/WAssert.h"
#include "core/common/WIOTools.h"
#include "core/common/WPropertyHelper.h"
#include "core/dataHandler/WDataSet.h"
#include "core/dataHandler/WDataSetSingle.h"
#include "core/dataHandler/WDataSetScalar.h"
#include "core/dataHandler/WDataSetTimeSeries.h"
#include "core/dataHandler/WDataSetVector.h"
#include "core/dataHandler/WSubject.h"
#include "core/dataHandler/WDataHandler.h"
#include "core/dataHandler/WDataTexture3D.h"
#include "core/dataHandler/WEEG2.h"
#include "core/dataHandler/exceptions/WDHException.h"
#include "core/graphicsEngine/WGEColormapping.h"
#include "core/kernel/WModuleOutputData.h"
#include "io/WReaderBiosig.h"
#include "io/WReaderEEGASCII.h"
#include "io/WReaderNIfTI.h"
#include "io/WReaderELC.h"
#include "io/WReaderFiberVTK.h"
#include "io/WReaderLibeep.h"
#include "io/WPagerEEGLibeep.h"
#include "WMData.h"
#include "WMData.xpm"
WMData::WMData():
WDataModule(),
m_fileNameSet( false ),
m_isTexture(),
m_transformNoMatrix( 4, 4 ),
m_transformSForm( 4, 4 ),
m_transformQForm( 4, 4 )
{
// initialize members
}
WMData::~WMData()
{
// cleanup
}
boost::shared_ptr< WModule > WMData::factory() const
{
return boost::shared_ptr< WModule >( new WMData() );
}
const char** WMData::getXPMIcon() const
{
return WMData_xpm;
}
const std::string WMData::getName() const
{
return "Data Module";
}
const std::string WMData::getDescription() const
{
return "This module encapsulates data.";
}
boost::shared_ptr< WDataSet > WMData::getDataSet()
{
return m_dataSet;
}
void WMData::setFilename( boost::filesystem::path fname )
{
if( !m_fileNameSet )
{
m_fileNameSet = true;
m_fileName = fname;
}
}
boost::filesystem::path WMData::getFilename() const
{
return m_fileName;
}
void WMData::connectors()
{
// initialize connectors
m_output= boost::shared_ptr< WModuleOutputData< WDataSet > >( new WModuleOutputData< WDataSet >(
shared_from_this(), "out", "A loaded dataset." )
);
// add it to the list of connectors. Please note, that a connector NOT added via addConnector will not work as expected.
addConnector( m_output );
// call WModules initialization
WDataModule::connectors();
}
void WMData::properties()
{
m_propCondition = boost::shared_ptr< WCondition >( new WCondition() );
// properties
m_dataName = m_infoProperties->addProperty( "Filename", "The filename of the dataset.", std::string( "" ) );
m_dataType = m_infoProperties->addProperty( "Data type", "The type of the the single data values.", std::string( "" ) );
m_matrixSelectionsList = boost::shared_ptr< WItemSelection >( new WItemSelection() );
m_matrixSelectionsList->addItem( "No matrix", "" );
m_matrixSelectionsList->addItem( "sform", "" );
m_matrixSelectionsList->addItem( "qform", "" );
m_matrixSelection = m_properties->addProperty( "Transformation matrix", "matrix",
m_matrixSelectionsList->getSelectorFirst(), m_propCondition );
WPropertyHelper::PC_SELECTONLYONE::addTo( m_matrixSelection );
// use this callback for the other properties
WPropertyBase::PropertyChangeNotifierType propertyCallback = boost::bind( &WMData::propertyChanged, this, _1 );
}
void WMData::propertyChanged( boost::shared_ptr< WPropertyBase > property )
{
if( m_isTexture )
{
if( property == m_active )
{
// forward to texture
m_dataSet->getTexture()->active()->set( m_active->get( true ) );
}
}
else
{
if( property == m_active )
{
if( m_active->get() )
{
m_output->updateData( m_dataSet );
}
else
{
m_output->updateData( boost::shared_ptr< WDataSet >() );
}
}
}
}
void WMData::moduleMain()
{
WAssert( m_fileNameSet, "No filename specified." );
m_transformNoMatrix.makeIdentity();
m_transformSForm.makeIdentity();
m_transformQForm.makeIdentity();
m_moduleState.setResetable( true, true );
m_moduleState.add( m_propCondition );
std::string fileName = m_fileName.string();
debugLog() << "Loading data from \"" << fileName << "\".";
m_dataName->set( fileName );
// remove the path up to the file name and set it as a convenient name for this module instance
if( fileName != "" )
{
m_runtimeName->set( string_utils::tokenize( fileName, "/" ).back() );
}
// load it now
std::string suffix = getSuffix( fileName );
if( suffix == ".nii"
|| ( suffix == ".gz" && ::nifti_compiled_with_zlib() ) )
{
if( suffix == ".gz" ) // it may be a NIfTI file too
{
boost::filesystem::path p( fileName );
p.replace_extension( "" );
suffix = getSuffix( p.string() );
WAssert( suffix == ".nii", "Currently only nii files may be gzipped." );
}
WReaderNIfTI niiLoader( fileName );
m_dataSet = niiLoader.load();
m_transformNoMatrix = niiLoader.getStandardTransform();
m_transformSForm = niiLoader.getSFormTransform();
m_transformQForm = niiLoader.getQFormTransform();
m_isTexture = m_dataSet->isTexture();
boost::shared_ptr< WDataSetSingle > dss = boost::shared_dynamic_cast< WDataSetSingle >( m_dataSet );
if( dss )
{
m_dataType->set( getDataTypeString( dss ) );
if( dss->isTexture() )
{
switch( (*dss).getValueSet()->getDataType() )
{
case W_DT_UNSIGNED_CHAR:
case W_DT_INT16:
case W_DT_UINT16:
case W_DT_UINT32:
case W_DT_SIGNED_INT:
m_dataSet->getTexture()->colormap()->set(
m_dataSet->getTexture()->colormap()->get().newSelector( WItemSelector::IndexList( 1, 0 ) )
);
break;
case W_DT_FLOAT:
case W_DT_DOUBLE:
if( boost::shared_dynamic_cast< WDataSetVector >( m_dataSet ) )
{
m_dataSet->getTexture()->colormap()->set(
m_dataSet->getTexture()->colormap()->get().newSelector( WItemSelector::IndexList( 1, 6 ) )
);
m_dataSet->getTexture()->interpolation()->set( false );
}
else
{
m_dataSet->getTexture()->colormap()->set(
m_dataSet->getTexture()->colormap()->get().newSelector( WItemSelector::IndexList( 1, 5 ) )
);
}
break;
default:
WAssert( false, "Could not load \"" + fileName + "\". Reason: unknown data type in Data module" );
}
}
}
}
else if( suffix == ".edf" )
{
WReaderBiosig biosigLoader( fileName );
m_dataSet = biosigLoader.load();
}
else if( suffix == ".asc" )
{
WReaderEEGASCII eegAsciiLoader( fileName );
m_dataSet = eegAsciiLoader.load();
}
else if( suffix == ".cnt" )
{
boost::shared_ptr< WPagerEEG > pager( new WPagerEEGLibeep( fileName ) );
std::string elcFileName = fileName;
elcFileName.resize( elcFileName.size() - 3 ); // drop suffix
elcFileName += "elc"; // add new suffix
WReaderELC elcReader( elcFileName );
boost::shared_ptr< WEEGPositionsLibrary > eegPositionsLibrary = elcReader.read();
m_dataSet = boost::shared_ptr< WEEG2 >( new WEEG2( pager, eegPositionsLibrary ) );
}
else if( suffix == ".fib" )
{
WReaderFiberVTK fibReader( fileName );
m_dataSet = fibReader.read();
}
else
{
throw WDHException( std::string( "Could not load \"" + fileName + "\". Reason: unknown file type: \"" + suffix + "\"" ) );
}
debugLog() << "Loading data done.";
// register the dataset properties
m_properties->addProperty( m_dataSet->getProperties() );
m_infoProperties->addProperty( m_dataSet->getInformationProperties() );
// I am interested in the active property ( manually subscribe signal )
m_active->getCondition()->subscribeSignal( boost::bind( &WMData::propertyChanged, this, m_active ) );
// textures also provide properties
if( m_dataSet->isTexture() )
{
if( !getSuppressColormaps() )
{
WGEColormapping::registerTexture( m_dataSet->getTexture(), m_runtimeName->get() );
}
m_properties->addProperty( m_dataSet->getTexture()->getProperties() );
m_infoProperties->addProperty( m_dataSet->getTexture()->getInformationProperties() );
}
// notify
m_output->updateData( m_dataSet );
ready();
WDataSetSingle::SPtr dataSetAsSingle = boost::shared_dynamic_cast< WDataSetSingle >( m_dataSet );
while( !m_shutdownFlag() )
{
m_moduleState.wait();
if( m_shutdownFlag() )
{
break;
}
// change transform matrix (only if we have a dataset single which contains the grid)
if( m_matrixSelection->changed() && dataSetAsSingle )
{
if( m_dataSet && m_isTexture )
{
// remove dataset from datahandler
if( m_dataSet->isTexture() )
{
m_properties->removeProperty( m_dataSet->getTexture()->getProperties() );
m_infoProperties->removeProperty( m_dataSet->getTexture()->getInformationProperties() );
WGEColormapping::deregisterTexture( m_dataSet->getTexture() );
}
}
// a new grid
boost::shared_ptr< WGrid > newGrid;
boost::shared_ptr< WGridRegular3D > oldGrid = boost::shared_dynamic_cast< WGridRegular3D >( dataSetAsSingle->getGrid() );
switch( m_matrixSelection->get( true ).getItemIndexOfSelected( 0 ) )
{
case 0:
newGrid = boost::shared_ptr< WGrid >( new WGridRegular3D( oldGrid->getNbCoordsX(), oldGrid->getNbCoordsY(), oldGrid->getNbCoordsZ(),
WGridTransformOrtho( m_transformNoMatrix ) ) );
break;
case 1:
newGrid = boost::shared_ptr< WGrid >( new WGridRegular3D( oldGrid->getNbCoordsX(), oldGrid->getNbCoordsY(), oldGrid->getNbCoordsZ(),
WGridTransformOrtho( m_transformSForm ) ) );
break;
case 2:
newGrid = boost::shared_ptr< WGrid >( new WGridRegular3D( oldGrid->getNbCoordsX(), oldGrid->getNbCoordsY(), oldGrid->getNbCoordsZ(),
WGridTransformOrtho( m_transformQForm ) ) );
break;
}
m_dataSet = dataSetAsSingle->clone( newGrid );
// the clone() may have returned a zero-pointer, only update if it hasn't
// this may happen if the clone() operation has not been implemented in the derived dataset class
if( m_dataSet )
{
m_output->updateData( m_dataSet );
if( m_isTexture )
{
if( !getSuppressColormaps() )
{
WGEColormapping::registerTexture( m_dataSet->getTexture(), m_runtimeName->get() );
}
m_properties->addProperty( m_dataSet->getTexture()->getProperties() );
m_infoProperties->addProperty( m_dataSet->getTexture()->getInformationProperties() );
}
}
}
}
// remove dataset from datahandler
if( m_dataSet->isTexture() )
{
m_properties->removeProperty( m_dataSet->getTexture()->getProperties() );
m_infoProperties->removeProperty( m_dataSet->getTexture()->getInformationProperties() );
WGEColormapping::deregisterTexture( m_dataSet->getTexture() );
}
}
// TODO(wiebel): move this to some central place.
std::string WMData::getDataTypeString( boost::shared_ptr< WDataSetSingle > dss )
{
std::string result;
switch( (*dss).getValueSet()->getDataType() )
{
case W_DT_NONE:
result = "none";
break;
case W_DT_BINARY:
result = "binary (1 bit)";
break;
case W_DT_UNSIGNED_CHAR:
result = "unsigned char (8 bits)";
break;
case W_DT_SIGNED_SHORT:
result = "signed short (16 bits)";
break;
case W_DT_SIGNED_INT:
result = "signed int (32 bits)";
break;
case W_DT_FLOAT:
result = "float (32 bits)";
break;
case W_DT_COMPLEX:
result = "complex";
break;
case W_DT_DOUBLE:
result = "double (64 bits)";
break;
case W_DT_RGB:
result = "RGB triple (24 bits)";
break;
case W_DT_ALL:
result = "ALL (not very useful)";
break;
case W_DT_INT8:
result = "signed char (8 bits)";
break;
case W_DT_UINT16:
result = "unsigned short (16 bits)";
break;
case W_DT_UINT32 :
result = "unsigned int (32 bits)";
break;
case W_DT_INT64:
result = "int64";
break;
case W_DT_UINT64:
result = "unsigned long long (64 bits)";
break;
case W_DT_FLOAT128:
result = "float (128 bits)";
break;
case W_DT_COMPLEX128:
result = "double pair (128 bits)";
break;
case W_DT_COMPLEX256:
result = " long double pair (256 bits)";
break;
case W_DT_RGBA32:
result = "4 byte RGBA (32 bits)";
break;
default:
WAssert( false, "Unknow data type in getDataTypeString" );
}
return result;
}
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