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Merge pull request #926 from CGSchwarzMayo/odt1
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antsApplyTransforms: add option -odt to set output datatype
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@ntustison
ntustison authored Jan 8, 2020
2 parents e00e816 + ca694d4 commit 5412eff
Showing 1 changed file with 154 additions and 12 deletions.
166 changes: 154 additions & 12 deletions Examples/antsApplyTransforms.cxx
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@
#include "itkResampleImageFilter.h"
#include "itkVectorImage.h"
#include "itkVectorIndexSelectionCastImageFilter.h"
#include "itkCastImageFilter.h"

#include "itkAffineTransform.h"
#include "itkCompositeTransform.h"
Expand Down Expand Up @@ -138,7 +139,7 @@ bool isDiagonalElement(std::vector<unsigned int> diagElements, unsigned int ind)
return false;
}

template <typename T, unsigned int Dimension>
template <typename T, unsigned int Dimension, typename OT>
int antsApplyTransforms( itk::ants::CommandLineParser::Pointer & parser, unsigned int inputImageType = 0 )
{
typedef T RealType;
Expand All @@ -158,6 +159,13 @@ int antsApplyTransforms( itk::ants::CommandLineParser::Pointer & parser, unsigne
typedef itk::VectorImage<PixelType, Dimension> MultiChannelImageType;
typedef itk::Image<TensorPixelType, Dimension> TensorImageType;

typedef OT OutputPixelType;
typedef itk::Image<OutputPixelType, Dimension> OutputImageType;
typedef itk::Image<OutputPixelType, Dimension + 1> OutputTimeSeriesImageType;
typedef itk::VectorImage<OutputPixelType, Dimension> OutputMultiChannelImageType;
typedef itk::Vector<OutputPixelType, Dimension> OutputVectorType;
typedef itk::Image<OutputVectorType, Dimension> OutputDisplacementFieldType;

typedef typename ants::RegistrationHelper<T, Dimension> RegistrationHelperType;
typedef typename RegistrationHelperType::AffineTransformType AffineTransformType;
typedef typename RegistrationHelperType::CompositeTransformType CompositeTransformType;
Expand Down Expand Up @@ -606,11 +614,18 @@ int antsApplyTransforms( itk::ants::CommandLineParser::Pointer & parser, unsigne
}
It.Set( vector );
}
typedef itk::ImageFileWriter<DisplacementFieldType> WriterType;

typedef itk::CastImageFilter<DisplacementFieldType, OutputDisplacementFieldType> CastFitlerType;
typename CastFitlerType::Pointer caster = CastFitlerType::New();
caster->SetInput( outputVectorImage );
caster->Update();

typedef itk::ImageFileWriter<OutputDisplacementFieldType> WriterType;
typename WriterType::Pointer writer = WriterType::New();
writer->SetInput( outputVectorImage );
writer->SetInput( caster->GetOutput() );
writer->SetFileName( ( outputFileName ).c_str() );
writer->Update();

}
else if( inputImageType == 2 )
{
Expand Down Expand Up @@ -707,19 +722,35 @@ int antsApplyTransforms( itk::ants::CommandLineParser::Pointer & parser, unsigne
}
if( inputImageType == 3 )
{
WriteImage<TimeSeriesImageType>( outputTimeSeriesImage, ( outputFileName ).c_str() );
typedef itk::CastImageFilter<TimeSeriesImageType, OutputTimeSeriesImageType> CastFitlerType;
typename CastFitlerType::Pointer caster = CastFitlerType::New();
caster->SetInput( outputTimeSeriesImage );
caster->Update();

WriteImage<OutputTimeSeriesImageType>( caster->GetOutput(), ( outputFileName ).c_str() );
}
else // inputImageType == 4
{
multiChannelImage = ConvertTimeSeriesImageToMultiChannelImage<TimeSeriesImageType, MultiChannelImageType>( outputTimeSeriesImage );
WriteImage<MultiChannelImageType>( multiChannelImage, ( outputFileName ).c_str() );

typedef itk::CastImageFilter<MultiChannelImageType, OutputMultiChannelImageType> CastFitlerType;
typename CastFitlerType::Pointer caster = CastFitlerType::New();
caster->SetInput( multiChannelImage );
caster->Update();

WriteImage<OutputMultiChannelImageType>( caster->GetOutput(), ( outputFileName ).c_str() );
}
}
else
{
try
{
WriteImage<ImageType>( outputImages[0], ( outputFileName ).c_str() );
typedef itk::CastImageFilter<ImageType, OutputImageType> CastFitlerType;
typename CastFitlerType::Pointer caster = CastFitlerType::New();
caster->SetInput( outputImages[0] );
caster->Update();

WriteImage<OutputImageType>( caster->GetOutput(), ( outputFileName ).c_str() );
}
catch( itk::ExceptionObject & err )
{
Expand Down Expand Up @@ -849,6 +880,31 @@ static void antsApplyTransformsInitializeCommandLineOptions( itk::ants::CommandL
parser->AddOption( option );
}

{
std::string description =
std::string( "Output image data type. " )
+ std::string( "This is a direct typecast; output values are not rescaled. " )
+ std::string( "Default is to use the internal data type (float or double). " )
+ std::string( "uchar is unsigned char; others are signed. " )
+ std::string( "WARNING: Outputs will be incorrect (overflowed/reinterpreted) " )
+ std::string( "if values exceed the range allowed by your choice. " )
+ std::string( "Note that some pixel types are not supported by some image " )
+ std::string( "formats. e.g. int is not supported by jpg. " );

OptionType::Pointer option = OptionType::New();
option->SetLongName( "output-data-type" );
option->SetShortName( 'u' );
option->SetUsageOption( 0, "char" );
option->SetUsageOption( 1, "uchar" );
option->SetUsageOption( 2, "short" );
option->SetUsageOption( 3, "int" );
option->SetUsageOption( 4, "float" );
option->SetUsageOption( 5, "double" );
option->SetUsageOption( 6, "default" );
option->SetDescription( description );
parser->AddOption( option );
}

{
std::string description =
std::string( "Several transform options are supported including all " )
Expand Down Expand Up @@ -1118,6 +1174,14 @@ int antsApplyTransforms( std::vector<std::string> args, std::ostream * /*out_str
}
}

std::string outputDataType( "default" );
typename itk::ants::CommandLineParser::OptionType::Pointer outputDataTypeOption = parser->GetOption( "output-data-type" );
if( outputDataTypeOption && outputDataTypeOption->GetNumberOfFunctions() )
{
outputDataType = outputDataTypeOption->GetFunction( 0 )->GetName();
ConvertToLowerCase( outputDataType );
}

switch( dimension )
{
case 2:
Expand All @@ -1134,11 +1198,37 @@ int antsApplyTransforms( std::vector<std::string> args, std::ostream * /*out_str
{
if( useDoublePrecision )
{
return antsApplyTransforms<double, 2>( parser, imageType );
if( !std::strcmp( outputDataType.c_str(), "char" ) )
return antsApplyTransforms<double, 2, char>( parser, imageType );
else if( !std::strcmp( outputDataType.c_str(), "uchar" ) )
return antsApplyTransforms<double, 2, unsigned char>( parser, imageType );
else if( !std::strcmp( outputDataType.c_str(), "short" ) )
return antsApplyTransforms<double, 2, short>( parser, imageType );
else if( !std::strcmp( outputDataType.c_str(), "int" ) )
return antsApplyTransforms<double, 2, int>( parser, imageType );
else if( !std::strcmp( outputDataType.c_str(), "float" ) )
return antsApplyTransforms<double, 2, float>( parser, imageType );
else if( !std::strcmp( outputDataType.c_str(), "double" ) )
return antsApplyTransforms<double, 2, double>( parser, imageType );
else
return antsApplyTransforms<double, 2, double>( parser, imageType );
}
else
{
return antsApplyTransforms<float, 2>( parser, imageType );
if( !std::strcmp( outputDataType.c_str(), "char" ) )
return antsApplyTransforms<float, 2, char>( parser, imageType );
else if( !std::strcmp( outputDataType.c_str(), "uchar" ) )
return antsApplyTransforms<float, 2, unsigned char>( parser, imageType );
else if( !std::strcmp( outputDataType.c_str(), "short" ) )
return antsApplyTransforms<float, 2, short>( parser, imageType );
else if( !std::strcmp( outputDataType.c_str(), "int" ) )
return antsApplyTransforms<float, 2, int>( parser, imageType );
else if( !std::strcmp( outputDataType.c_str(), "float" ) )
return antsApplyTransforms<float, 2, float>( parser, imageType );
else if( !std::strcmp( outputDataType.c_str(), "double" ) )
return antsApplyTransforms<float, 2, double>( parser, imageType );
else
return antsApplyTransforms<float, 2, float>( parser, imageType );
}
}
}
Expand All @@ -1147,11 +1237,37 @@ int antsApplyTransforms( std::vector<std::string> args, std::ostream * /*out_str
{
if( useDoublePrecision )
{
return antsApplyTransforms<double, 3>( parser, imageType );
if( !std::strcmp( outputDataType.c_str(), "char" ) )
return antsApplyTransforms<double, 3, char>( parser, imageType );
else if( !std::strcmp( outputDataType.c_str(), "uchar" ) )
return antsApplyTransforms<double, 3, unsigned char>( parser, imageType );
else if( !std::strcmp( outputDataType.c_str(), "short" ) )
return antsApplyTransforms<double, 3, short>( parser, imageType );
else if( !std::strcmp( outputDataType.c_str(), "int" ) )
return antsApplyTransforms<double, 3, int>( parser, imageType );
else if( !std::strcmp( outputDataType.c_str(), "float" ) )
return antsApplyTransforms<double, 3, float>( parser, imageType );
else if( !std::strcmp( outputDataType.c_str(), "double" ) )
return antsApplyTransforms<double, 3, double>( parser, imageType );
else
return antsApplyTransforms<double, 3, double>( parser, imageType );
}
else
{
return antsApplyTransforms<float, 3>( parser, imageType );
if( !std::strcmp( outputDataType.c_str(), "char" ) )
return antsApplyTransforms<float, 3, char>( parser, imageType );
else if( !std::strcmp( outputDataType.c_str(), "uchar" ) )
return antsApplyTransforms<float, 3, unsigned char>( parser, imageType );
else if( !std::strcmp( outputDataType.c_str(), "short" ) )
return antsApplyTransforms<float, 3, short>( parser, imageType );
else if( !std::strcmp( outputDataType.c_str(), "int" ) )
return antsApplyTransforms<float, 3, int>( parser, imageType );
else if( !std::strcmp( outputDataType.c_str(), "float" ) )
return antsApplyTransforms<float, 3, float>( parser, imageType );
else if( !std::strcmp( outputDataType.c_str(), "double" ) )
return antsApplyTransforms<float, 3, double>( parser, imageType );
else
return antsApplyTransforms<float, 3, float>( parser, imageType );
}
}
break;
Expand All @@ -1175,11 +1291,37 @@ int antsApplyTransforms( std::vector<std::string> args, std::ostream * /*out_str
{
if( useDoublePrecision )
{
return antsApplyTransforms<double, 4>( parser, imageType );
if( !std::strcmp( outputDataType.c_str(), "char" ) )
return antsApplyTransforms<double, 4, char>( parser, imageType );
else if( !std::strcmp( outputDataType.c_str(), "uchar" ) )
return antsApplyTransforms<double, 4, unsigned char>( parser, imageType );
else if( !std::strcmp( outputDataType.c_str(), "short" ) )
return antsApplyTransforms<double, 4, short>( parser, imageType );
else if( !std::strcmp( outputDataType.c_str(), "int" ) )
return antsApplyTransforms<double, 4, int>( parser, imageType );
else if( !std::strcmp( outputDataType.c_str(), "float" ) )
return antsApplyTransforms<double, 4, float>( parser, imageType );
else if( !std::strcmp( outputDataType.c_str(), "double" ) )
return antsApplyTransforms<double, 4, double>( parser, imageType );
else
return antsApplyTransforms<double, 4, double>( parser, imageType );
}
else
{
return antsApplyTransforms<float, 4>( parser, imageType );
if( !std::strcmp( outputDataType.c_str(), "char" ) )
return antsApplyTransforms<float, 4, char>( parser, imageType );
else if( !std::strcmp( outputDataType.c_str(), "uchar" ) )
return antsApplyTransforms<float, 4, unsigned char>( parser, imageType );
else if( !std::strcmp( outputDataType.c_str(), "short" ) )
return antsApplyTransforms<float, 4, short>( parser, imageType );
else if( !std::strcmp( outputDataType.c_str(), "int" ) )
return antsApplyTransforms<float, 4, int>( parser, imageType );
else if( !std::strcmp( outputDataType.c_str(), "float" ) )
return antsApplyTransforms<float, 4, float>( parser, imageType );
else if( !std::strcmp( outputDataType.c_str(), "double" ) )
return antsApplyTransforms<float, 4, double>( parser, imageType );
else
return antsApplyTransforms<float, 4, float>( parser, imageType );
}
}
}
Expand Down

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