#include <cpPlugins/Plugins/ImageReader.h>
#include <cpPlugins/Interface/Image.h>
-#include <itkImageFileReader.h>
+#include <set>
-#define ITK_MANUAL_INSTANTIATION
-#include <itkImage.h>
-#include <itkRGBPixel.h>
+#include <itkImageFileReader.h>
+#include <itkImageSeriesReader.h>
// -------------------------------------------------------------------------
cpPlugins::Plugins::ImageReader::
ImageReader( )
: Superclass( )
{
+ this->m_ClassName = "cpPlugins::ImageReader";
+ this->m_ClassCategory = "ImageReader";
+
this->SetNumberOfOutputs( 1 );
this->_MakeOutput< cpPlugins::Interface::Image >( 0 );
- this->m_DefaultParameters[ "FileName" ] =
- TParameter( "string", "no_file_name" );
- this->m_DefaultParameters[ "PixelType" ] = TParameter( "type", "uchar" );
- this->m_DefaultParameters[ "ImageDimension" ] = TParameter( "int", "2" );
- this->m_DefaultParameters[ "IsColorImage" ] = TParameter( "bool", "0" );
+ using namespace cpPlugins::Interface;
+ this->m_DefaultParameters.Configure( Parameters::StringList, "FileNames" );
+ this->m_Parameters = this->m_DefaultParameters;
}
// -------------------------------------------------------------------------
{
}
-// -------------------------------------------------------------------------
-std::string cpPlugins::Plugins::ImageReader::
-GetClassName( ) const
-{
- return( "cpPlugins::Plugins::ImageReader" );
-}
-
// -------------------------------------------------------------------------
std::string cpPlugins::Plugins::ImageReader::
_GenerateData( )
{
- TParameters::const_iterator dIt;
+ // Get filenames
+ TStringList names;
+ this->m_Parameters.GetValueAsStringList( names, "FileNames" );
- // Get image dimension
- dIt = this->m_Parameters.find( "ImageDimension" );
- if( dIt == this->m_Parameters.end( ) )
- dIt = this->m_DefaultParameters.find( "ImageDimension" );
-
- std::string ret = "itk::Image dimension not supported.";
- if ( dIt->second.second == "1" ) ret = this->_GenerateData0< 1 >( );
- else if( dIt->second.second == "2" ) ret = this->_GenerateData0< 2 >( );
- else if( dIt->second.second == "3" ) ret = this->_GenerateData0< 3 >( );
- else if( dIt->second.second == "4" ) ret = this->_GenerateData0< 4 >( );
+ std::string r = "";
+ if( names.size( ) >= 1 )
+ {
+ // Guess image properties
+ itk::ImageIOBase::Pointer io =
+ itk::ImageIOFactory::CreateImageIO(
+ names[ 0 ].c_str( ),
+ itk::ImageIOFactory::ReadMode
+ );
+ if( io.IsNotNull( ) )
+ {
+ io->SetFileName( names[ 0 ] );
+ io->ReadImageInformation( );
+ if( names.size( ) == 1 )
+ {
+ switch( io->GetNumberOfDimensions( ) )
+ {
+ case 2: r = this->_GD0< 2 >( io, names ); break;
+ case 3: r = this->_GD0< 3 >( io, names ); break;
+ case 4: r = this->_GD0< 4 >( io, names ); break;
+ default:
+ r = "ImageReader: Single image dimension not supported.";
+ break;
+ } // hctiws
+ }
+ else if( names.size( ) > 1 )
+ {
+ switch( io->GetNumberOfDimensions( ) )
+ {
+ case 1: r = this->_GD0< 2 >( io, names ); break;
+ case 2: r = this->_GD0< 3 >( io, names ); break;
+ case 3: r = this->_GD0< 4 >( io, names ); break;
+ default:
+ r = "ImageReader: Multiple images dimension not supported.";
+ break;
+ } // hctiws
- return( ret );
+ } // fi
+ }
+ else
+ r = "ImageReader: Could not CreateImageIO for \"" + names[ 0 ] + "\"";
+ }
+ else
+ r = "No image files given";
+ return( r );
}
// -------------------------------------------------------------------------
template< unsigned int D >
std::string cpPlugins::Plugins::ImageReader::
-_GenerateData0( )
+_GD0( itk::ImageIOBase* io, const TStringList& names )
{
- TParameters::const_iterator tIt, cIt;
-
- // Get image pixelType
- tIt = this->m_Parameters.find( "PixelType" );
- if( tIt == this->m_Parameters.end( ) )
- tIt = this->m_DefaultParameters.find( "PixelType" );
- cIt = this->m_Parameters.find( "IsColorImage" );
- if( cIt == this->m_Parameters.end( ) )
- cIt = this->m_DefaultParameters.find( "IsColorImage" );
-
- std::string ret = "itk::Image pixel type not supported";
- if( cIt->second.second == "0" )
+ itk::ImageIOBase::IOComponentType ct = io->GetComponentType( );
+ itk::ImageIOBase::IOPixelType pt = io->GetPixelType( );
+ std::string r = "";
+
+ if( pt == itk::ImageIOBase::SCALAR )
+ {
+ switch( ct )
+ {
+ case itk::ImageIOBase::UCHAR:
+ r = this->_RealGD< unsigned char, D >( names );
+ break;
+ case itk::ImageIOBase::CHAR:
+ r = this->_RealGD< char, D >( names );
+ break;
+ case itk::ImageIOBase::USHORT:
+ r = this->_RealGD< unsigned short, D >( names );
+ break;
+ case itk::ImageIOBase::SHORT:
+ r = this->_RealGD< short, D >( names );
+ break;
+ case itk::ImageIOBase::UINT:
+ r = this->_RealGD< unsigned int, D >( names );
+ break;
+ case itk::ImageIOBase::INT:
+ r = this->_RealGD< int, D >( names );
+ break;
+ case itk::ImageIOBase::ULONG:
+ r = this->_RealGD< unsigned long, D >( names );
+ break;
+ case itk::ImageIOBase::LONG:
+ r = this->_RealGD< long, D >( names );
+ break;
+ case itk::ImageIOBase::FLOAT:
+ r = this->_RealGD< float, D >( names );
+ break;
+ case itk::ImageIOBase::DOUBLE:
+ r = this->_RealGD< double, D >( names );
+ break;
+ default:
+ r = "ImageReader: Scalar pixel type not supported.";
+ break;
+ } // hctiws
+ }
+ else if( pt == itk::ImageIOBase::RGB )
+ {
+ if( D == 2 )
+ {
+ switch( ct )
+ {
+ case itk::ImageIOBase::UCHAR:
+ r = this->_RealGD< itk::RGBPixel< unsigned char >, 2 >( names );
+ break;
+ case itk::ImageIOBase::CHAR:
+ r = this->_RealGD< itk::RGBPixel< char >, 2 >( names );
+ break;
+ case itk::ImageIOBase::USHORT:
+ r = this->_RealGD< itk::RGBPixel< unsigned short >, 2 >( names );
+ break;
+ case itk::ImageIOBase::SHORT:
+ r = this->_RealGD< itk::RGBPixel< short >, 2 >( names );
+ break;
+ default:
+ r = "ImageReader: Scalar pixel type not supported.";
+ break;
+ } // hctiws
+ }
+ else if( D == 3 )
+ {
+ switch( ct )
+ {
+ case itk::ImageIOBase::UCHAR:
+ r = this->_RealGD< itk::RGBPixel< unsigned char >, 3 >( names );
+ break;
+ case itk::ImageIOBase::CHAR:
+ r = this->_RealGD< itk::RGBPixel< char >, 3 >( names );
+ break;
+ case itk::ImageIOBase::USHORT:
+ r = this->_RealGD< itk::RGBPixel< unsigned short >, 3 >( names );
+ break;
+ case itk::ImageIOBase::SHORT:
+ r = this->_RealGD< itk::RGBPixel< short >, 3 >( names );
+ break;
+ default:
+ r = "ImageReader: Scalar pixel type not supported.";
+ break;
+ } // hctiws
+ }
+ else if( D == 4 )
+ {
+ switch( ct )
+ {
+ case itk::ImageIOBase::UCHAR:
+ r = this->_RealGD< itk::RGBPixel< unsigned char >, 4 >( names );
+ break;
+ case itk::ImageIOBase::CHAR:
+ r = this->_RealGD< itk::RGBPixel< char >, 4 >( names );
+ break;
+ case itk::ImageIOBase::USHORT:
+ r = this->_RealGD< itk::RGBPixel< unsigned short >, 4 >( names );
+ break;
+ case itk::ImageIOBase::SHORT:
+ r = this->_RealGD< itk::RGBPixel< short >, 4 >( names );
+ break;
+ default:
+ r = "ImageReader: Scalar pixel type not supported.";
+ break;
+ } // hctiws
+
+ } // fi
+ }
+ else if( pt == itk::ImageIOBase::RGBA )
+ {
+ if( D == 2 )
+ {
+ switch( ct )
+ {
+ case itk::ImageIOBase::UCHAR:
+ r = this->_RealGD< itk::RGBAPixel< unsigned char >, 2 >( names );
+ break;
+ case itk::ImageIOBase::CHAR:
+ r = this->_RealGD< itk::RGBAPixel< char >, 2 >( names );
+ break;
+ case itk::ImageIOBase::USHORT:
+ r = this->_RealGD< itk::RGBAPixel< unsigned short >, 2 >( names );
+ break;
+ case itk::ImageIOBase::SHORT:
+ r = this->_RealGD< itk::RGBAPixel< short >, 2 >( names );
+ break;
+ default:
+ r = "ImageReader: Scalar pixel type not supported.";
+ break;
+ } // hctiws
+ }
+ else if( D == 3 )
+ {
+ switch( ct )
+ {
+ case itk::ImageIOBase::UCHAR:
+ r = this->_RealGD< itk::RGBAPixel< unsigned char >, 3 >( names );
+ break;
+ case itk::ImageIOBase::CHAR:
+ r = this->_RealGD< itk::RGBAPixel< char >, 3 >( names );
+ break;
+ case itk::ImageIOBase::USHORT:
+ r = this->_RealGD< itk::RGBAPixel< unsigned short >, 3 >( names );
+ break;
+ case itk::ImageIOBase::SHORT:
+ r = this->_RealGD< itk::RGBAPixel< short >, 3 >( names );
+ break;
+ default:
+ r = "ImageReader: Scalar pixel type not supported.";
+ break;
+ } // hctiws
+ }
+ else if( D == 4 )
+ {
+ switch( ct )
+ {
+ case itk::ImageIOBase::UCHAR:
+ r = this->_RealGD< itk::RGBAPixel< unsigned char >, 4 >( names );
+ break;
+ case itk::ImageIOBase::CHAR:
+ r = this->_RealGD< itk::RGBAPixel< char >, 4 >( names );
+ break;
+ case itk::ImageIOBase::USHORT:
+ r = this->_RealGD< itk::RGBAPixel< unsigned short >, 4 >( names );
+ break;
+ case itk::ImageIOBase::SHORT:
+ r = this->_RealGD< itk::RGBAPixel< short >, 4 >( names );
+ break;
+ default:
+ r = "ImageReader: Scalar pixel type not supported.";
+ break;
+ } // hctiws
+
+ } // fi
+ }
+ else if( pt == itk::ImageIOBase::OFFSET )
{
- if( tIt->second.second == "char" )
- ret = this->_GenerateData1< char, D >( );
- else if( tIt->second.second == "short" )
- ret = this->_GenerateData1< short, D >( );
- else if( tIt->second.second == "int" )
- ret = this->_GenerateData1< int, D >( );
- else if( tIt->second.second == "long" )
- ret = this->_GenerateData1< long, D >( );
- else if( tIt->second.second == "uchar" )
- ret = this->_GenerateData1< unsigned char, D >( );
- else if( tIt->second.second == "ushort" )
- ret = this->_GenerateData1< unsigned short, D >( );
- else if( tIt->second.second == "uint" )
- ret = this->_GenerateData1< unsigned int, D >( );
- else if( tIt->second.second == "ulong" )
- ret = this->_GenerateData1< unsigned long, D >( );
- else if( tIt->second.second == "float" )
- ret = this->_GenerateData1< float, D >( );
- else if( tIt->second.second == "double" )
- ret = this->_GenerateData1< double, D >( );
+ switch( D )
+ {
+ case 2:
+ r = this->_RealGD< itk::Offset< 2 >, 2 >( names );
+ break;
+ case 3:
+ r = this->_RealGD< itk::Offset< 3 >, 3 >( names );
+ break;
+ case 4:
+ r = this->_RealGD< itk::Offset< 4 >, 4 >( names );
+ break;
+ default:
+ r = "ImageReader: Offset pixel dimension not supported.";
+ break;
+ } // hctiws
}
- else if( cIt->second.second == "1" )
+ else if( pt == itk::ImageIOBase::VECTOR )
{
- if( tIt->second.second == "char" )
- ret = this->_GenerateData1< itk::RGBPixel< char >, D >( );
- else if( tIt->second.second == "short" )
- ret = this->_GenerateData1< itk::RGBPixel< short >, D >( );
- else if( tIt->second.second == "int" )
- ret = this->_GenerateData1< itk::RGBPixel< int >, D >( );
- else if( tIt->second.second == "long" )
- ret = this->_GenerateData1< itk::RGBPixel< long >, D >( );
- else if( tIt->second.second == "uchar" )
- ret = this->_GenerateData1< itk::RGBPixel< unsigned char >, D >( );
- else if( tIt->second.second == "ushort" )
- ret = this->_GenerateData1< itk::RGBPixel< unsigned short >, D >( );
- else if( tIt->second.second == "uint" )
- ret = this->_GenerateData1< itk::RGBPixel< unsigned int >, D >( );
- else if( tIt->second.second == "ulong" )
- ret = this->_GenerateData1< itk::RGBPixel< unsigned long >, D >( );
- else if( tIt->second.second == "float" )
- ret = this->_GenerateData1< itk::RGBPixel< float >, D >( );
- else if( tIt->second.second == "double" )
- ret = this->_GenerateData1< itk::RGBPixel< double >, D >( );
- } // fi
- return( ret );
+ switch( ct )
+ {
+ case itk::ImageIOBase::FLOAT:
+ r = this->_RealGD< itk::Vector< float, D >, D >( names );
+ break;
+ case itk::ImageIOBase::DOUBLE:
+ r = this->_RealGD< itk::Vector< double, D >, D >( names );
+ break;
+ default:
+ r = "ImageReader: Vector type not supported.";
+ break;
+ } // hctiws
+ }
+ else if( pt == itk::ImageIOBase::POINT )
+ {
+ switch( ct )
+ {
+ case itk::ImageIOBase::FLOAT:
+ r = this->_RealGD< itk::Point< float, D >, D >( names );
+ break;
+ case itk::ImageIOBase::DOUBLE:
+ r = this->_RealGD< itk::Point< double, D >, D >( names );
+ break;
+ default:
+ r = "ImageReader: Point type not supported.";
+ break;
+ } // hctiws
+ }
+ else if( pt == itk::ImageIOBase::COVARIANTVECTOR )
+ {
+ switch( ct )
+ {
+ case itk::ImageIOBase::FLOAT:
+ r = this->_RealGD< itk::CovariantVector< float, D >, D >( names );
+ break;
+ case itk::ImageIOBase::DOUBLE:
+ r = this->_RealGD< itk::CovariantVector< double, D >, D >( names );
+ break;
+ default:
+ r = "ImageReader: Vector type not supported.";
+ break;
+ } // hctiws
+ }
+ else if( pt == itk::ImageIOBase::SYMMETRICSECONDRANKTENSOR )
+ {
+ switch( ct )
+ {
+ case itk::ImageIOBase::FLOAT:
+ r =
+ this->_RealGD< itk::SymmetricSecondRankTensor< float, D >, D >(
+ names
+ );
+ break;
+ case itk::ImageIOBase::DOUBLE:
+ r =
+ this->_RealGD< itk::SymmetricSecondRankTensor< double, D >, D >(
+ names
+ );
+ break;
+ default:
+ r = "ImageReader: Vector type not supported.";
+ break;
+ } // hctiws
+ }
+ else if( pt == itk::ImageIOBase::DIFFUSIONTENSOR3D )
+ {
+ if( D == 3 )
+ {
+ switch( ct )
+ {
+ case itk::ImageIOBase::FLOAT:
+ r = this->_RealGD< itk::DiffusionTensor3D< float >, 3 >( names );
+ break;
+ case itk::ImageIOBase::DOUBLE:
+ r = this->_RealGD< itk::DiffusionTensor3D< double >, 3 >( names );
+ break;
+ default:
+ r = "ImageReader: Diffusion tensor type not supported.";
+ break;
+ } // hctiws
+ }
+ else
+ r = "ImageReader: Diffusion tensor dimension not supported.";
+ }
+ else if( pt == itk::ImageIOBase::COMPLEX )
+ {
+ switch( ct )
+ {
+ case itk::ImageIOBase::FLOAT:
+ r = this->_RealGD< std::complex< float >, D >( names );
+ break;
+ case itk::ImageIOBase::DOUBLE:
+ r = this->_RealGD< std::complex< double >, D >( names );
+ break;
+ default:
+ r = "ImageReader: Complex type not supported.";
+ break;
+ } // hctiws
+ }
+ else
+ r = "ImageReader: Image pixel type not yet supported.";
+ /* TODO
+ itk::ImageIOBase::FIXEDARRAY
+ itk::ImageIOBase::MATRIX
+ */
+
+ return( r );
}
// -------------------------------------------------------------------------
template< class P, unsigned int D >
std::string cpPlugins::Plugins::ImageReader::
-_GenerateData1( )
+_RealGD( const TStringList& names )
{
- TParameters::const_iterator fIt;
-
- // Get image pixelType
- fIt = this->m_Parameters.find( "FileName" );
- if( fIt == this->m_Parameters.end( ) )
- fIt = this->m_DefaultParameters.find( "FileName" );
+ typedef itk::Image< P, D > _I;
- typedef itk::Image< P, D > _TImage;
- typedef itk::ImageFileReader< _TImage > _TImageReader;
-
- _TImageReader* reader =
- dynamic_cast< _TImageReader* >( this->m_Reader.GetPointer( ) );
- if( reader == NULL )
+ std::string r = "";
+ if( names.size( ) == 1 )
{
- this->m_Reader = _TImageReader::New( );
- reader = dynamic_cast< _TImageReader* >( this->m_Reader.GetPointer( ) );
+ // Read single image
+ typedef itk::ImageFileReader< _I > _SR;
+ _SR* reader =
+ dynamic_cast< _SR* >( this->m_RealProcessObject.GetPointer( ) );
+ if( reader == NULL )
+ {
+ this->m_RealProcessObject = _SR::New( );
+ reader =
+ dynamic_cast< _SR* >( this->m_RealProcessObject.GetPointer( ) );
- } // fi
- reader->SetFileName( fIt->second.second );
- try
- {
- reader->Update( );
+ } // fi
+ reader->SetFileName( names[ 0 ] );
+ try
+ {
+ reader->Update( );
+ cpPlugins::Interface::Image* out =
+ this->_Output< cpPlugins::Interface::Image >( 0 );
+ if( out != NULL )
+ out->SetITKImage< _I >( reader->GetOutput( ) );
+ else
+ r = "ImageReader: output not correctly created.";
+ }
+ catch( itk::ExceptionObject& err )
+ {
+ r = "ImageReader: " + std::string( err.GetDescription( ) );
+ cpPlugins::Interface::Image* out =
+ this->_Output< cpPlugins::Interface::Image >( 0 );
+ if( out != NULL )
+ out->SetITKImage< _I >( NULL );
+ else
+ r = "ImageReader: output not correctly created.";
+
+ } // yrt
}
- catch( itk::ExceptionObject& err )
+ else if( names.size( ) > 1 )
{
- return( err.GetDescription( ) );
+ // Read image series
+ std::set< std::string > ordered_names;
+ for( unsigned int i = 0; i < names.size( ); ++i )
+ ordered_names.insert( names[ i ] );
+
+ typedef itk::ImageSeriesReader< _I > _MR;
+ _MR* reader =
+ dynamic_cast< _MR* >( this->m_RealProcessObject.GetPointer( ) );
+ if( reader == NULL )
+ {
+ this->m_RealProcessObject = _MR::New( );
+ reader =
+ dynamic_cast< _MR* >( this->m_RealProcessObject.GetPointer( ) );
- } // yrt
- this->_SetOutput( 0, reader->GetOutput( ) );
- return( "" );
+ } // fi
+ std::set< std::string >::const_iterator fnIt = ordered_names.begin( );
+ for( ; fnIt != ordered_names.end( ); ++fnIt )
+ reader->AddFileName( *fnIt );
+ try
+ {
+ reader->Update( );
+ cpPlugins::Interface::Image* out =
+ this->_Output< cpPlugins::Interface::Image >( 0 );
+ if( out != NULL )
+ out->SetITKImage< _I >( reader->GetOutput( ) );
+ else
+ r = "ImageReader: output not correctly created.";
+ }
+ catch( itk::ExceptionObject& err )
+ {
+ r = "ImageReader: " + std::string( err.GetDescription( ) );
+ cpPlugins::Interface::Image* out =
+ this->_Output< cpPlugins::Interface::Image >( 0 );
+ if( out != NULL )
+ out->SetITKImage< _I >( NULL );
+ else
+ r = "ImageReader: output not correctly created.";
+
+ } // yrt
+ }
+ else
+ r = "ImageReader: No image files given";
+ return( r );
}
// eof - $RCSfile$
git://git.creatis.insa-lyon.fr / cpPlugins.git / blobdiff