Examples/IO/ImageReadImageSeriesWrite.cxx

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//  Software Guide : BeginLatex
//
//  This example illustrates how to save an image using the
//  \doxygen{ImageSeriesWriter}. This class enables the saving of a 3D volume as a set
//  of files containing one 2D slice per file.
//
//  \index{itk::ImageFileReader!header}
//  \index{itk::ImageSeriesWriter!header}
//
//  Software Guide : EndLatex


#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageSeriesWriter.h"
#include "itkNumericSeriesFileNames.h"

int main( int argc, char *argv[] )
{
  if (argc < 4 )
    {
    std::cerr << "Usage: ImageReadImageSeriesWrite inputFile outputPrefix outputExtension" << std::endl;
    return EXIT_FAILURE;
    }

  //  Software Guide : BeginLatex
  //
  //  The type of the input image is declared here and it is used for declaring
  //  the type of the reader. This will be a conventional 3D image reader.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using ImageType = itk::Image< unsigned char, 3 >;
  using ReaderType = itk::ImageFileReader< ImageType >;
  // Software Guide : EndCodeSnippet

  //  Software Guide : BeginLatex
  //
  //  The reader object is constructed using the \code{New()} operator and
  //  assigning the result to a \code{SmartPointer}. The filename of the 3D
  //  volume to be read is taken from the command line arguments and passed to
  //  the reader using the \code{SetFileName()} method.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  ReaderType::Pointer reader = ReaderType::New();
  reader->SetFileName( argv[1] );
  // Software Guide : EndCodeSnippet

  //  Software Guide : BeginLatex
  //
  //  The type of the series writer must be instantiated taking into account that
  //  the input file is a 3D volume and the output files are 2D images.
  //  Additionally, the output of the reader is connected as input to the writer.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using Image2DType = itk::Image< unsigned char, 2 >;

  using WriterType = itk::ImageSeriesWriter< ImageType, Image2DType >;

  WriterType::Pointer writer = WriterType::New();

  writer->SetInput( reader->GetOutput() );
  // Software Guide : EndCodeSnippet

  //  Software Guide : BeginLatex
  //
  //  The writer requires a list of filenames to be generated. This list can be
  //  produced with the help of the \doxygen{NumericSeriesFileNames} class.
  //
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using NameGeneratorType = itk::NumericSeriesFileNames;

  NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
  // Software Guide : EndCodeSnippet

  //  Software Guide : BeginLatex
  //
  //  The \code{NumericSeriesFileNames} class requires an input string in order
  //  to have a template for generating the filenames of all the output slices.
  //  Here we compose this string using a prefix taken from the command line
  //  arguments and adding the extension for PNG files.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  std::string format = argv[2];
  format += "%03d.";
  format += argv[3];   // filename extension

  nameGenerator->SetSeriesFormat( format.c_str() );
  // Software Guide : EndCodeSnippet

  //  Software Guide : BeginLatex
  //
  //  The input string is going to be used for generating filenames by setting
  //  the values of the first and last slice. This can be done by collecting
  //  information from the input image. Note that before attempting to take any
  //  image information from the reader, its execution must be triggered with
  //  the invocation of the \code{Update()} method, and since this invocation
  //  can potentially throw exceptions, it must be put inside a
  //  \code{try/catch} block.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  try
    {
    reader->Update();
    }
  catch( itk::ExceptionObject & excp )
    {
    std::cerr << "Exception thrown while reading the image" << std::endl;
    std::cerr << excp << std::endl;
    }
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // Now that the image has been read we can query its largest possible region
  // and recover information about the number of pixels along every dimension.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  ImageType::ConstPointer inputImage = reader->GetOutput();
  ImageType::RegionType   region     = inputImage->GetLargestPossibleRegion();
  ImageType::IndexType    start      = region.GetIndex();
  ImageType::SizeType     size       = region.GetSize();
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // With this information we can find the number that will identify the first
  // and last slices of the 3D data set. These numerical values are then passed to
  // the filename generator object that will compose the names of the files
  // where the slices are going to be stored.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  const unsigned int firstSlice = start[2];
  const unsigned int lastSlice  = start[2] + size[2] - 1;

  nameGenerator->SetStartIndex( firstSlice );
  nameGenerator->SetEndIndex( lastSlice );
  nameGenerator->SetIncrementIndex( 1 );
  // Software Guide : EndCodeSnippet

  //  Software Guide : BeginLatex
  //
  //  The list of filenames is taken from the names generator and it is passed to
  //  the series writer.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  writer->SetFileNames( nameGenerator->GetFileNames() );
  // Software Guide : EndCodeSnippet

  //  Software Guide : BeginLatex
  //
  //  Finally we trigger the execution of the pipeline with the \code{Update()}
  //  method on the writer. At this point the slices of the image will be saved
  //  in individual files containing a single slice per file. The filenames used
  //  for these slices are those produced by the filename generator.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  try
    {
    writer->Update();
    }
  catch( itk::ExceptionObject & excp )
    {
    std::cerr << "Exception thrown while reading the image" << std::endl;
    std::cerr << excp << std::endl;
    }
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // Note that by saving data into isolated slices we are losing information
  // that may be significant for medical applications, such as the interslice
  // spacing in millimeters.
  //
  // Software Guide : EndLatex

  return EXIT_SUCCESS;
}