ITK  5.0.0
Insight Segmentation and Registration Toolkit
Examples/IO/CovariantVectorImageExtractComponent.cxx
/*=========================================================================
*
* Copyright Insight Software Consortium
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*=========================================================================*/
// Software Guide : BeginLatex
//
// This example illustrates how to read an image whose pixel type is
// \code{CovariantVector}, extract one of its components to form a scalar
// image and finally save this image into a file.
//
// The \doxygen{VectorIndexSelectionCastImageFilter} is used to extract
// a scalar from the vector image. It is also possible to cast the component
// type when using this filter. It is the user's responsibility to make sure
// that the cast will not result in any information loss.
//
// Let's start by including the relevant header files.
//
// \index{itk::ImageFileRead!Vector images}
// \index{itk::Vector\-Index\-Selection\-Cast\-Image\-Filter!header}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
// Software Guide : EndCodeSnippet
#include "itkImage.h"
int main( int argc, char ** argv )
{
// Verify the number of parameters in the command line
if( argc < 4 )
{
std::cerr << "Usage: " << std::endl;
std::cerr << argv[0] << " inputVectorImageFile outputScalarImageFile";
std::cerr << " outupNormalizedScalarImageFile";
std::cerr << " componentToExtract" << std::endl;
return EXIT_FAILURE;
}
// Software Guide : BeginLatex
//
// We read an image of \doxygen{CovariantVector} pixels and extract one of
// its components to generate a scalar image of a consistent pixel type.
// Then, we rescale the intensities of this scalar image and write it as an
// image of \code{unsigned short} pixels.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using ComponentType = float;
constexpr unsigned int Dimension = 2;
using InputPixelType = itk::CovariantVector< ComponentType,
Dimension >;
using OutputPixelType = unsigned short;
using ComponentImageType = itk::Image< ComponentType, Dimension >;
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The \doxygen{ImageFileReader} and \doxygen{ImageFileWriter}
// are instantiated using the image types.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The VectorIndexSelectionCastImageFilter is instantiated
// using the input and output image types. A filter object is created with
// the \code{New()} method and assigned to a \doxygen{SmartPointer}.
//
// \index{itk::Vector\-Index\-Selection\-Cast\-Image\-Filter!Instantiation}
// \index{itk::Vector\-Index\-Selection\-Cast\-Image\-Filter!New()}
// \index{itk::Vector\-Index\-Selection\-Cast\-Image\-Filter!Pointer}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
InputImageType,
ComponentImageType >;
FilterType::Pointer componentExtractor = FilterType::New();
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The VectorIndexSelectionCastImageFilter class requires us to specify
// which of the vector components is to be extracted from the vector image.
// This is done with the \code{SetIndex()} method. In this example we obtain
// this value from the command line arguments.
//
// \index{itk::Vector\-Index\-Selection\-Cast\-Image\-Filter!SetIndex()}
//
// Software Guide : EndLatex
const unsigned int indexOfComponentToExtract = std::stoi( argv[4] );
if( indexOfComponentToExtract >= Dimension )
{
std::cerr << "You are requesting an index out of the range for the Vector dimension" << std::endl;
std::cerr << "Vector dimension is = " << Dimension << std::endl;
std::cerr << "but your requested index = " << indexOfComponentToExtract << std::endl;
return EXIT_FAILURE;
}
// Software Guide : BeginCodeSnippet
componentExtractor->SetIndex( indexOfComponentToExtract );
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The \doxygen{RescaleIntensityImageFilter} filter is instantiated here.
//
// \index{RescaleIntensityImageFilter!Instantiation}
// \index{RescaleIntensityImageFilter!New()}
// \index{RescaleIntensityImageFilter!Pointer}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using RescaleFilterType = itk::RescaleIntensityImageFilter<
ComponentImageType,
OutputImageType >;
RescaleFilterType::Pointer rescaler = RescaleFilterType::New();
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The minimum and maximum values for the output image are specified in
// the following. Note the use of the \doxygen{NumericTraits} class which
// allows us to define a number of type-related constants in a generic
// way. The use of traits is a fundamental characteristic of generic
// programming~\cite{Austern1999,Alexandrescu2001}.
//
// \index{RescaleIntensityImageFilter!SetOutputMinimum()}
// \index{RescaleIntensityImageFilter!SetOutputMaximum()}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
rescaler->SetOutputMinimum( itk::NumericTraits< OutputPixelType >::min() );
rescaler->SetOutputMaximum( itk::NumericTraits< OutputPixelType >::max() );
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Below, we create the reader and writer using the \code{New()} method and
// assign the result to a \doxygen{SmartPointer}.
//
// \index{itk::ImageFileReader!New()}
// \index{itk::ImageFileWriter!New()}
// \index{itk::ImageFileReader!SmartPointer}
// \index{itk::ImageFileWriter!SmartPointer}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
ReaderType::Pointer reader = ReaderType::New();
WriterType::Pointer writer = WriterType::New();
// Software Guide : EndCodeSnippet
// Here we recover the file names from the command line arguments
//
const char * inputFilename = argv[1];
const char * outputFilename = argv[3];
// Software Guide : BeginLatex
//
// The name of the file to be read or written is passed to the
// \code{SetFileName()} method.
//
// \index{itk::ImageFileReader!SetFileName()}
// \index{itk::ImageFileWriter!SetFileName()}
// \index{SetFileName()!itk::ImageFileReader}
// \index{SetFileName()!itk::ImageFileWriter}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
reader->SetFileName( inputFilename );
writer->SetFileName( outputFilename );
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Below we connect the reader, filter and writer to form the data
// processing pipeline.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
componentExtractor->SetInput( reader->GetOutput() );
rescaler->SetInput( componentExtractor->GetOutput() );
writer->SetInput( rescaler->GetOutput() );
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Finally we execute the pipeline by invoking \code{Update()} on the
// writer. The call is placed in a \code{try/catch} block in case exceptions
// are thrown.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
try
{
writer->Update();
}
catch( itk::ExceptionObject & err )
{
std::cerr << "ExceptionObject caught !" << std::endl;
std::cerr << err << std::endl;
return EXIT_FAILURE;
}
// Software Guide : EndCodeSnippet
// Here We add another writer that will produce the non-normalized output
// file
//
using ComponentWriterType = itk::ImageFileWriter< ComponentImageType >;
ComponentWriterType::Pointer componentWriter = ComponentWriterType::New();
componentWriter->SetInput( componentExtractor->GetOutput() );
componentWriter->SetFileName( argv[2] );
componentWriter->Update();
return EXIT_SUCCESS;
}