text: /*=========================================================================
   *
   *  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 a series of 2D slices from independent
  //  files in order to compose a volume. The class \doxygen{ImageSeriesReader}
  //  is used for this purpose. This class works in combination with a generator
  //  of filenames that will provide a list of files to be read. In this
  //  particular example we use the \doxygen{RegularExpressionSeriesFileNames} class as
  //  filename generator. This generator uses a regular expression for generating a list
  //  of filenames. The filenames are then ordered according to sub expression.
  //
  // Regular expressions are a powerful,  compact mechanism for parsing strings.
  // Expressions consist of the following metacharacters:
  //
  // \begin{itemize}
  //
  //  \item \^        Matches at beginning of a line
  //
  //  \item \$        Matches at end of a line
  //
  //  \item \.         Matches any single character
  //
  //  \item  \[ \]       Matches any character(s) inside the brackets
  //
  //  \item  \[\^ \]      Matches any character(s) not inside the brackets
  //
  //  \item \-        Matches any character in range on either side of a dash
  //
  //  \item \*        Matches preceding pattern zero or more times
  //
  //  \item \+        Matches preceding pattern one or more times
  //
  //  \item \?        Matches preceding pattern zero or once only
  //
  //  \item \(\)        Saves a matched expression and uses it in a  later match
  // \begin{itemize}
  //
  // Note that more than one of these metacharacters can be  used in  a  single
  // regular expression in order to create complex search patterns. For example,
  // the pattern \{ [^ab1-9] }  says  to match  any  character  sequence that
  // does not begin with the characters "ab"  followed  by  numbers  in  the
  // series  one through nine.
  //
  //
  // In order to use the RegularExpressionSeriesFileNames class we should include
  // the following headers as shown.
  //
  //  \index{itk::ImageSeriesReader!header}
  //  \index{itk::RegularExpressionSeriesFileNames!header}
  //
  //  Software Guide : EndLatex
  
  // Software Guide : BeginCodeSnippet
  #include "itkImage.h"
  #include "itkImageSeriesReader.h"
  #include "itkImageFileWriter.h"
  #include "itkRegularExpressionSeriesFileNames.h"
  #include "itkPNGImageIO.h"
  // Software Guide : EndCodeSnippet
  
  
  int main( int argc, char ** argv )
  {
    // Verify the number of parameters in the command line
    if( argc < 5 )
      {
      std::cerr << "Usage: " << std::endl;
      std::cerr << argv[0] << "directory regularExression ";
      std::cerr << "sortingExpression outputImageFile " << std::endl;
      return EXIT_FAILURE;
      }
  
  
    // Software Guide : BeginLatex
    //
    // We start by defining the \code{PixelType} and \code{ImageType}.
    //
    //
    // Software Guide : EndLatex
  
    // Software Guide : BeginCodeSnippet
    typedef unsigned char                       PixelType;
    const unsigned int Dimension = 3;
  
    typedef itk::Image< PixelType, Dimension >  ImageType;
    // Software Guide : EndCodeSnippet
  
  
    // Software Guide : BeginLatex
    //
    // The image type is used as a template parameter to instantiate
    // the reader and writer.
    //
    // \index{itk::ImageSeriesReader!Instantiation}
    // \index{itk::ImageFileWriter!Instantiation}
    //
    // Software Guide : EndLatex
  
    // Software Guide : BeginCodeSnippet
    typedef itk::ImageSeriesReader< ImageType >  ReaderType;
    typedef itk::ImageFileWriter<   ImageType >  WriterType;
  
    ReaderType::Pointer reader = ReaderType::New();
    WriterType::Pointer writer = WriterType::New();
    // Software Guide : EndCodeSnippet
  
  
    std::string directory = argv[1];
    std::string regularExpression = argv[2];
  
    const unsigned int subMatch = atoi( argv[3] );
  
    std::string outputFilename = argv[4];
  
  
    // Software Guide : BeginLatex
    //
    // Then, we declare the filenames generator type and create one instance of it.
    //
    // Software Guide : EndLatex
  
    // Software Guide : BeginCodeSnippet
    typedef itk::RegularExpressionSeriesFileNames    NameGeneratorType;
  
    NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
    // Software Guide : EndCodeSnippet
  
  
    // Software Guide : BeginLatex
    //
    // The filenames generator requires us to provide a pattern of text for the
    // regular expression, the sorting expression, as well as the directory where
    // the files are stored.
    //
    // Software Guide : EndLatex
  
    // Software Guide : BeginCodeSnippet
    nameGenerator->SetRegularExpression( regularExpression );
    nameGenerator->SetSubMatch( subMatch );
  
    nameGenerator->SetDirectory( directory );
    // Software Guide : EndCodeSnippet
  
    //  Software Guide : BeginLatex
    //
    //  The ImageIO object that actually performs the read process is now connected
    //  to the ImageSeriesReader. This is the safest way of making sure that we use
    //  an ImageIO object that is appropriate for the type of files that we want to
    //  read.
    //
    //  Software Guide : EndLatex
  
    // Software Guide : BeginCodeSnippet
    reader->SetImageIO( itk::PNGImageIO::New() );
    // Software Guide : EndCodeSnippet
  
    //  Software Guide : BeginLatex
    //
    //  The filenames of the input files must be provided to the reader. While the
    //  writer is instructed to write the same volume dataset in a single file.
    //
    //
    //  Software Guide : EndLatex
  
    // Software Guide : BeginCodeSnippet
    reader->SetFileNames( nameGenerator->GetFileNames()  );
  
    writer->SetFileName( outputFilename );
    // Software Guide : EndCodeSnippet
  
    // Software Guide : BeginLatex
    //
    // We connect the output of the reader to the input of the writer.
    //
    // Software Guide : EndLatex
  
    // Software Guide : BeginCodeSnippet
    writer->SetInput( reader->GetOutput() );
    // Software Guide : EndCodeSnippet
  
  
    //  Software Guide : BeginLatex
    //
    //  Finally, execution of the pipeline can be triggered by invoking the
    //  Update() method in the writer. This call must be placed in a try/catch
    //  block since exceptions be potentially be thrown in the process of reading
    //  or writing the images.
    //
    //  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
  
    return EXIT_SUCCESS;
  }
  