Commit 11452c24 authored by reichenbach's avatar reichenbach
Browse files

[FIX] removed HARDIEXtractor files

parent 85179250
FILE( GLOB_RECURSE MODULES_SRC "*.cpp" "*.h" )
# Unit tests
IF( OW_COMPILE_TESTS )
CXXTEST_ADD_TESTS_FROM_LIST( "${MODULES_SRC}"
"kernel"
)
ENDIF( OW_COMPILE_TESTS )
/* XPM */
static const char * HARDIExtractor_xpm[] = {
"32 32 5 1",
" c #FFFFFF",
". c #D2D2D2",
"+ c #9C9C9C",
"@ c #6C6C6C",
"# c #3C3C3C",
" ",
" .............. ",
" .............. ",
" .............. ",
" ++++++++++++++. ",
" ++++++++++++++. ",
" ++++++++++++++. ",
" ++++++++++++++. ",
" ++++++++++++++. ",
" ++++++++++++++. ",
" ++++++++++++++. ",
" +++++++++@@@@@@@@@@@@@@ ",
" ##############@@@@@@@@@@@ ",
" ##############@@@@@@@@@@@ ",
" ##############@@@@@@@@@@@ ",
" ##############@@@@@@@@@@@ ",
" ##############@@@@@@@@@@@ ",
" ##############@@@@@@@@@@@ ",
" ##############@@@@@@@@@@@ ",
" ##############@@@@@@@@@@@ ",
" ##############@@@@@@@@@@@ ",
" ##############@@@@@@@@@@@ ",
" ##############@@@@@@@@@@@ ",
" ##############@@@@@@@@@@@ ",
" ##############@@@@@@@@@@@ ",
" ##############@@@@@@@@@@@ ",
" ##############@@@@@@@@@@@ ",
" ##############@@@@@@@@@@@ ",
" ##############@@@@@@@@@@@ ",
" ##############@@@@@@@@@@@ ",
" ##############@@@@@@@@@@@ ",
" ############## "};
//---------------------------------------------------------------------------
//
// Project: OpenWalnut ( http://www.openwalnut.org )
//
// Copyright 2009 OpenWalnut Community, BSV-Leipzig and CNCF-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 <sstream>
#include <vector>
#include "../../kernel/WKernel.h"
#include "../../dataHandler/WDataHandler.h"
#include "HARDIExtractor.xpm"
#include "WMHARDIExtractor.h"
WMHARDIExtractor::WMHARDIExtractor():
WModule()
{
}
WMHARDIExtractor::~WMHARDIExtractor()
{
}
boost::shared_ptr< WModule > WMHARDIExtractor::factory() const
{
return boost::shared_ptr< WModule >( new WMHARDIExtractor() );
}
const std::string WMHARDIExtractor::getName() const
{
return "HARDI Extractor";
}
const std::string WMHARDIExtractor::getDescription() const
{
return "This module allows extracting of single images from a HARDI dataset.";
}
const char** WMHARDIExtractor::getXPMIcon() const
{
return HARDIExtractor_xpm;
}
void WMHARDIExtractor::connectors()
{
m_input = boost::shared_ptr< WModuleInputData < WDataSetRawHARDI > >(
new WModuleInputData< WDataSetRawHARDI >( shared_from_this(), "in", "The HARDI dataset." ) );
addConnector( m_input );
m_output = boost::shared_ptr< WModuleOutputData < WDataSetScalar > >(
new WModuleOutputData< WDataSetScalar >( shared_from_this(), "out", "The extracted image." ) );
addConnector( m_output );
WModule::connectors();
}
void WMHARDIExtractor::properties()
{
m_propCondition = boost::shared_ptr< WCondition >( new WCondition() );
m_selectedImage = m_properties->addProperty( "Image", "The image to be extracted.", 0, m_propCondition );
m_selectedImage->setMin( 0 );
m_selectedImage->setMax( 1 );
}
void WMHARDIExtractor::moduleMain()
{
m_moduleState.setResetable( true, true );
m_moduleState.add( m_input->getDataChangedCondition() );
m_moduleState.add( m_propCondition );
ready();
while( !m_shutdownFlag() )
{
m_moduleState.wait();
if( m_shutdownFlag() )
{
break;
}
boost::shared_ptr< WDataSetRawHARDI > newDataSet = m_input->getData();
bool dataChanged = ( m_dataSet != newDataSet );
bool dataValid = ( newDataSet );
if( dataChanged && dataValid )
{
m_dataSet = newDataSet;
m_selectedImage->setMax( m_dataSet->getMeasures() - 1 );
m_selectedImage->ensureValidity( 0 );
}
if( dataValid )
{
if( m_outData )
{
WDataHandler::deregisterDataSet( m_outData );
}
std::size_t i = static_cast< std::size_t >( m_selectedImage->get( true ) );
m_outData = extract( i );
m_outData->setFileName( makeImageName( i ) );
m_output->updateData( m_outData );
if( m_outData )
{
WDataHandler::registerDataSet( m_outData );
}
}
}
if( m_outData )
{
WDataHandler::deregisterDataSet( m_outData );
}
}
boost::shared_ptr< WDataSetScalar > WMHARDIExtractor::extract( std::size_t i ) const
{
WAssert( m_dataSet, "" );
WAssert( m_dataSet->getValueSet(), "" );
WAssert( m_dataSet->getGrid(), "" );
if( i >= m_dataSet->getMeasures() )
{
return boost::shared_ptr< WDataSetScalar >();
}
boost::shared_ptr< WGridRegular3D > grid = boost::shared_dynamic_cast< WGridRegular3D >( m_dataSet->getGrid() );
WAssert( grid, "" );
switch( m_dataSet->getValueSet()->getDataType() )
{
case W_DT_FLOAT:
{
std::vector< float > values( m_dataSet->getGrid()->size() );
boost::shared_ptr< WValueSet< float > > v = boost::shared_dynamic_cast< WValueSet< float > >( m_dataSet->getValueSet() );
WAssert( v, "" );
for( std::size_t k = 0; k < grid->size(); ++k )
{
values[ k ] = v->rawData()[ m_dataSet->getMeasures() * k + i ];
}
boost::shared_ptr< WValueSet< float > > vs =
boost::shared_ptr< WValueSet< float > >( new WValueSet< float >( 0, 1, values, W_DT_FLOAT ) );
return boost::shared_ptr< WDataSetScalar >( new WDataSetScalar( vs, grid ) );
}
case W_DT_DOUBLE:
{
std::vector< double > values( m_dataSet->getGrid()->size() );
boost::shared_ptr< WValueSet< double > > v = boost::shared_dynamic_cast< WValueSet< double > >( m_dataSet->getValueSet() );
WAssert( v, "" );
for( std::size_t k = 0; k < grid->size(); ++k )
{
values[ k ] = v->rawData()[ m_dataSet->getMeasures() * k + i ];
}
boost::shared_ptr< WValueSet< double > > vs =
boost::shared_ptr< WValueSet< double > >( new WValueSet< double >( 0, 1, values, W_DT_DOUBLE ) );
return boost::shared_ptr< WDataSetScalar >( new WDataSetScalar( vs, grid ) );
}
case W_DT_UINT8:
{
std::vector< unsigned char > values( m_dataSet->getGrid()->size() );
boost::shared_ptr< WValueSet< unsigned char > > v = boost::shared_dynamic_cast< WValueSet< unsigned char > >( m_dataSet->getValueSet() );
WAssert( v, "" );
for( std::size_t k = 0; k < grid->size(); ++k )
{
values[ k ] = v->rawData()[ m_dataSet->getMeasures() * k + i ];
}
boost::shared_ptr< WValueSet< unsigned char > > vs =
boost::shared_ptr< WValueSet< unsigned char > >( new WValueSet< unsigned char >( 0, 1, values, W_DT_UINT8 ) );
return boost::shared_ptr< WDataSetScalar >( new WDataSetScalar( vs, grid ) );
}
case W_DT_UINT16:
{
std::vector< uint16_t > values( m_dataSet->getGrid()->size() );
boost::shared_ptr< WValueSet< uint16_t > > v = boost::shared_dynamic_cast< WValueSet< uint16_t > >( m_dataSet->getValueSet() );
WAssert( v, "" );
for( std::size_t k = 0; k < grid->size(); ++k )
{
values[ k ] = v->rawData()[ m_dataSet->getMeasures() * k + i ];
}
boost::shared_ptr< WValueSet< uint16_t > > vs =
boost::shared_ptr< WValueSet< uint16_t > >( new WValueSet< uint16_t >( 0, 1, values, W_DT_UINT16 ) );
return boost::shared_ptr< WDataSetScalar >( new WDataSetScalar( vs, grid ) );
}
case W_DT_UINT32:
{
std::vector< unsigned int > values( m_dataSet->getGrid()->size() );
boost::shared_ptr< WValueSet< unsigned int > > v = boost::shared_dynamic_cast< WValueSet< unsigned int > >( m_dataSet->getValueSet() );
WAssert( v, "" );
for( std::size_t k = 0; k < grid->size(); ++k )
{
values[ k ] = v->rawData()[ m_dataSet->getMeasures() * k + i ];
}
boost::shared_ptr< WValueSet< unsigned int > > vs =
boost::shared_ptr< WValueSet< unsigned int > >( new WValueSet< unsigned int >( 0, 1, values, W_DT_UINT32 ) );
return boost::shared_ptr< WDataSetScalar >( new WDataSetScalar( vs, grid ) );
}
case W_DT_INT8:
{
std::vector< char > values( m_dataSet->getGrid()->size() );
boost::shared_ptr< WValueSet< char > > v = boost::shared_dynamic_cast< WValueSet< char > >( m_dataSet->getValueSet() );
WAssert( v, "" );
for( std::size_t k = 0; k < grid->size(); ++k )
{
values[ k ] = v->rawData()[ m_dataSet->getMeasures() * k + i ];
}
boost::shared_ptr< WValueSet< char > > vs =
boost::shared_ptr< WValueSet< char > >( new WValueSet< char >( 0, 1, values, W_DT_INT8 ) );
return boost::shared_ptr< WDataSetScalar >( new WDataSetScalar( vs, grid ) );
}
case W_DT_INT16:
{
std::vector< int16_t > values( m_dataSet->getGrid()->size() );
boost::shared_ptr< WValueSet< int16_t > > v = boost::shared_dynamic_cast< WValueSet< int16_t > >( m_dataSet->getValueSet() );
WAssert( v, "" );
for( std::size_t k = 0; k < grid->size(); ++k )
{
values[ k ] = v->rawData()[ m_dataSet->getMeasures() * k + i ];
}
boost::shared_ptr< WValueSet< int16_t > > vs =
boost::shared_ptr< WValueSet< int16_t > >( new WValueSet< int16_t >( 0, 1, values, W_DT_INT16 ) );
return boost::shared_ptr< WDataSetScalar >( new WDataSetScalar( vs, grid ) );
}
case W_DT_SIGNED_INT:
{
std::vector< int > values( m_dataSet->getGrid()->size() );
boost::shared_ptr< WValueSet< int > > v = boost::shared_dynamic_cast< WValueSet< int > >( m_dataSet->getValueSet() );
WAssert( v, "" );
for( std::size_t k = 0; k < grid->size(); ++k )
{
values[ k ] = v->rawData()[ m_dataSet->getMeasures() * k + i ];
}
boost::shared_ptr< WValueSet< int > > vs =
boost::shared_ptr< WValueSet< int > >( new WValueSet< int >( 0, 1, values, W_DT_SIGNED_INT ) );
return boost::shared_ptr< WDataSetScalar >( new WDataSetScalar( vs, grid ) );
}
default:
warnLog() << "Encountered unsupported data format in HARDIExtractor!";
return boost::shared_ptr< WDataSetScalar >();
}
}
const std::string WMHARDIExtractor::makeImageName( std::size_t i )
{
std::stringstream s;
WAssert( m_dataSet, "" );
s << m_dataSet->getFileName() << " (" << ( i + 1 ) << " of " << m_dataSet->getMeasures() << ")";
return s.str();
}
//---------------------------------------------------------------------------
//
// Project: OpenWalnut ( http://www.openwalnut.org )
//
// Copyright 2009 OpenWalnut Community, BSV-Leipzig and CNCF-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 WMHARDIEXTRACTOR_H
#define WMHARDIEXTRACTOR_H
#include <string>
#include "../../kernel/WModule.h"
#include "../../kernel/WModuleInputData.h"
#include "../../kernel/WModuleOutputData.h"
#include "../../dataHandler/WDataSetScalar.h"
#include "../../dataHandler/WDataSetRawHARDI.h"
#include "../../dataHandler/WValueSet.h"
/**
* This module extracts single images fram a HARDI dataset.
*
* \ingroup modules
*/
class WMHARDIExtractor: public WModule
{
public:
/**
* Standard constructor.
*/
WMHARDIExtractor();
/**
* Destructor.
*/
virtual ~WMHARDIExtractor();
/**
* Gives back the name of this module.
* \return the module's name.
*/
virtual const std::string getName() const;
/**
* Gives back a description of this module.
* \return description to module.
*/
virtual const std::string getDescription() const;
/**
* Due to the prototype design pattern used to build modules, this method returns a new instance of this method. NOTE: it
* should never be initialized or modified in some other way. A simple new instance is required.
*
* \return the prototype used to create every module in OpenWalnut.
*/
virtual boost::shared_ptr< WModule > factory() const;
/**
* Return an icon for this module.
*
* \return the icon
*/
virtual const char** getXPMIcon() const;
protected:
/**
* Entry point after loading the module. Runs in separate thread.
*/
virtual void moduleMain();
/**
* Initialize the connectors this module is using.
*/
virtual void connectors();
/**
* Initialize the properties for this module.
*/
virtual void properties();
private:
/**
* Extract the ith image from the HARDI dataset. If there is no
* ith image, an invalid pointer will be returned.
*
* \param i The number of the image to be extracted.
* \return A pointer to extracted image as a scalar dataset or an invalid pointer, if no ith image exists.
*/
boost::shared_ptr< WDataSetScalar > extract( std::size_t i ) const;
/**
* Create a name for the extracted image.
*
* \param i The number of the image.
* \return The name.
*/
const std::string makeImageName( std::size_t i );
/**
* A property that allows selecting the number of the desired image.
*/
WPropInt m_selectedImage;
/**
* An input connector that accepts HARDI datasets.
*/
boost::shared_ptr< WModuleInputData< WDataSetRawHARDI > > m_input;
/**
* An output connector for the output scalar dsataset.
*/
boost::shared_ptr< WModuleOutputData< WDataSetScalar > > m_output;
/**
* This is a pointer to the dataset the module is currently working on.
*/
boost::shared_ptr< WDataSetRawHARDI > m_dataSet;
/**
* This is a pointer to the current output.
*/
boost::shared_ptr< WDataSetScalar > m_outData;
/**
* A condition used to notify about changes in several properties.
*/
boost::shared_ptr< WCondition > m_propCondition;
};
#endif // WMHARDIEXTRACTOR_H
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