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N4 verbosity #978

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N4 verbosity #978

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46 changes: 39 additions & 7 deletions Examples/N4BiasFieldCorrection.cxx
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Original file line number Diff line number Diff line change
Expand Up @@ -71,28 +71,44 @@ int N4( itk::ants::CommandLineParser *parser )
{
using RealType = float;

using ImageType = itk::Image<RealType, ImageDimension>;
typename ImageType::Pointer inputImage = nullptr;

using MaskImageType = itk::Image<RealType, ImageDimension>;
typename MaskImageType::Pointer maskImage = nullptr;

bool verbose = false;
typename itk::ants::CommandLineParser::OptionType::Pointer verboseOption =
parser->GetOption( "verbose" );
if( verboseOption && verboseOption->GetNumberOfFunctions() )
{
verbose = parser->Convert<bool>( verboseOption->GetFunction( 0 )->GetName() );
}
if( verbose )
{
std::cout << std::endl << "Creating ImageType" << std::endl;
}
using ImageType = itk::Image<RealType, ImageDimension>;
typename ImageType::Pointer inputImage = nullptr;

if( verbose )
{
std::cout << std::endl << "Creating MaskImageType" << std::endl;
}
using MaskImageType = itk::Image<RealType, ImageDimension>;
typename MaskImageType::Pointer maskImage = nullptr;

if( verbose )
{
std::cout << std::endl << "Running N4 for "
<< ImageDimension << "-dimensional images." << std::endl << std::endl;
}

if( verbose )
{
std::cout << std::endl << "Getting CorrecterType" << std::endl;
}
using CorrecterType = itk::N4BiasFieldCorrectionImageFilter<ImageType, MaskImageType, ImageType>;
typename CorrecterType::Pointer correcter = CorrecterType::New();

if( verbose )
{
std::cout << std::endl << "Reading in Input Image" << std::endl;
}
typename itk::ants::CommandLineParser::OptionType::Pointer inputImageOption =
parser->GetOption( "input-image" );
if( inputImageOption && inputImageOption->GetNumberOfFunctions() )
Expand All @@ -117,9 +133,17 @@ int N4( itk::ants::CommandLineParser *parser )

typename itk::ants::CommandLineParser::OptionType::Pointer maskImageOption =
parser->GetOption( "mask-image" );
if( maskImageOption && maskImageOption->GetNumberOfFunctions() )
if( verbose )
{
std::cout << std::endl << "maskImageOption: " << maskImageOption << std::endl;
}
if( maskImageOption && maskImageOption->GetNumberOfFunctions() )
{
std::string inputMaskFile = maskImageOption->GetFunction( 0 )->GetName();
if( verbose )
{
std::cout << std::endl << "Reading in Mask file: " << inputMaskFile << std::endl;
}
ReadImage<MaskImageType>( maskImage, inputMaskFile.c_str() );

isMaskImageSpecified = true;
Expand All @@ -140,6 +164,10 @@ int N4( itk::ants::CommandLineParser *parser )
/**
* check for negative values in the masked region
*/
if( verbose )
{
std::cout << std::endl << "Checking for Negative Values" << std::endl;
}
using ThresholderType = itk::BinaryThresholdImageFilter<MaskImageType, MaskImageType>;
typename ThresholderType::Pointer thresholder = ThresholderType::New();
thresholder->SetInsideValue( itk::NumericTraits<typename MaskImageType::PixelType>::ZeroValue() );
Expand All @@ -148,6 +176,10 @@ int N4( itk::ants::CommandLineParser *parser )
thresholder->SetUpperThreshold( itk::NumericTraits<typename MaskImageType::PixelType>::ZeroValue() );
thresholder->SetInput( maskImage );

if( verbose )
{
std::cout << std::endl << "Running LabelStatisticsImageFilter" << std::endl;
}
using StatsType = itk::LabelStatisticsImageFilter<ImageType, MaskImageType>;
typename StatsType::Pointer statsOriginal = StatsType::New();
statsOriginal->SetInput( inputImage );
Expand Down