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 the common task of extracting a 2D slice from a
  //  3D volume. Perform some processing on that slice and then paste it on an
  //  output volume of the same size as the volume from the input.
  //
  //  In this example we start by including the appropriate header files.
  //
  //  Software Guide : EndLatex
  // Software Guide : BeginCodeSnippet
  #include "itkImageFileReader.h"
  #include "itkImageFileWriter.h"
  // Software Guide : EndCodeSnippet
  
  //  Software Guide : BeginLatex
  //
  //  The filter used to extract a region from an image is the
  //  \doxygen{ExtractImageFilter}. Its header is included below.  This filter
  //  is capable of extracting a slice from the input image.
  //
  //  \index{itk::ExtractImageFilter!header}
  //
  //  Software Guide : EndLatex
  // Software Guide : BeginCodeSnippet
  #include "itkExtractImageFilter.h"
  // Software Guide : EndCodeSnippet
  
  //  Software Guide : BeginLatex
  //
  //  The filter used to place the processed image in a region of the output
  //  image is the \doxygen{PasteImageFilter}. Its header is included below.
  //  This filter is capable of inserting the processed image into the
  //  destination image.
  //
  //  \index{itk::PasteImageFilter!header}
  //
  //  Software Guide : EndLatex
  // Software Guide : BeginCodeSnippet
  #include "itkPasteImageFilter.h"
  // Software Guide : EndCodeSnippet
  // Software Guide : BeginCodeSnippet
  #include "itkMedianImageFilter.h"
  // Software Guide : EndCodeSnippet
  int main( int argc, char ** argv )
  {
    // Verify the number of parameters in the command line
    if( argc < 3 )
      {
      std::cerr << "Usage: " << std::endl;
      std::cerr << argv[0] << " input3DImageFile  output3DImageFile " << std::endl;
      std::cerr << " sliceNumber " << std::endl;
      return EXIT_FAILURE;
      }
  
    //  Software Guide : BeginLatex
    //
    //  Image types are defined below. Note that the input image type is $3D$ and
    //  the output image type is a $3D$ image as well.
    //
    //  Software Guide : EndLatex
    // Software Guide : BeginCodeSnippet
    typedef unsigned char                       InputPixelType;
    typedef unsigned char                       MiddlePixelType;
    typedef unsigned char                       OutputPixelType;
    typedef itk::Image< InputPixelType,  3 >    InputImageType;
    typedef itk::Image< MiddlePixelType, 3 >    MiddleImageType;
    typedef itk::Image< OutputPixelType, 3 >    OutputImageType;
    // Software Guide : EndCodeSnippet
  
    //  Software Guide : BeginLatex
    //
    //  The types for the \doxygen{ImageFileReader} and \doxygen{ImageFileWriter}
    //  are instantiated using the image types.
    //
    //  Software Guide : EndLatex
    // Software Guide : BeginCodeSnippet
    typedef itk::ImageFileReader< InputImageType  >  ReaderType;
    typedef itk::ImageFileWriter< OutputImageType >  WriterType;
    // Software Guide : EndCodeSnippet
  
    // Here we recover the file names from the command line arguments
    //
    const char * inputFilename  = argv[1];
    const char * outputFilename = argv[2];
  
    //  Software Guide : BeginLatex
    //
    //  Below, we create the reader and writer  using the New() method and
    //  assigning 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
  
    //  Software Guide : BeginLatex
    //
    //  The name of the file to be read or written is passed with the
    //  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
    //
    //  The ExtractImageFilter type is instantiated using the input and
    //  output image types. A filter object is created with the New()
    //  method and assigned to a SmartPointer.
    //
    //  Software Guide : EndLatex
    // Software Guide : BeginCodeSnippet
    typedef itk::ExtractImageFilter< InputImageType, MiddleImageType > ExtractFilterType;
    ExtractFilterType::Pointer extractFilter = ExtractFilterType::New();
    extractFilter->SetDirectionCollapseToSubmatrix();
    // Software Guide : EndCodeSnippet
  
    //  Software Guide : BeginLatex
    //
    //  The ExtractImageFilter requires a region to be defined by the user. The
    //  region is specified by an \doxygen{Index} indicating the pixel where the
    //  region starts and an \doxygen{Size} indication how many pixels the region
    //  has along each dimension. In order to extract a $2D$ image from a $3D$
    //  data set, it is enough to set the size of the region to $1$ in one
    //  dimension. Note that, strictly speaking, we are extracting here a $3D$
    //  image of a single slice. Here we take the region from the buffered region
    //  of the input image. Note that Update() is being called first on the
    //  reader, since otherwise the output would have invalid data.
    //
    //  Software Guide : EndLatex
  
    // Software Guide : BeginCodeSnippet
    reader->Update();
    const InputImageType * inputImage = reader->GetOutput();
    InputImageType::RegionType inputRegion = inputImage->GetBufferedRegion();
    // Software Guide : EndCodeSnippet
  
    //  Software Guide : BeginLatex
    //
    //  We take the size from the region and collapse the size in the $Z$
    //  component by setting its value to $1$.
    //
    //  Software Guide : EndLatex
    // Software Guide : BeginCodeSnippet
    InputImageType::SizeType size = inputRegion.GetSize();
    size[2] = 1;
    // Software Guide : EndCodeSnippet
    //  Software Guide : BeginLatex
    //
    //  Note that in this case we are extracting a $Z$ slice, and for that
    //  reason, the dimension to be collapsed in the one with index $2$. You
    //  may keep in mind the association of index components
    //  $\{X=0,Y=1,Z=2\}$. If we were interested in extracting a slice
    //  perpendicular to the $Y$ axis we would have set \code{size[1]=1;}.
    //
    //  Software Guide : EndLatex
  
    //  Software Guide : BeginLatex
    //
    //  Then, we take the index from the region and set its $Z$ value to the
    //  slice number we want to extract. In this example we obtain the slice
    //  number from the command line arguments.
    //
    //  Software Guide : EndLatex
    // Software Guide : BeginCodeSnippet
    InputImageType::IndexType start = inputRegion.GetIndex();
    const unsigned int sliceNumber = atoi( argv[3] );
    start[2] = sliceNumber;
    // Software Guide : EndCodeSnippet
  
    //  Software Guide : BeginLatex
    //
    //  Finally, an \doxygen{ImageRegion} object is created and initialized with
    //  the start and size we just prepared using the slice information.
    //
    //  Software Guide : EndLatex
    // Software Guide : BeginCodeSnippet
    InputImageType::RegionType desiredRegion;
    desiredRegion.SetSize(  size  );
    desiredRegion.SetIndex( start );
    // Software Guide : EndCodeSnippet
  
    //  Software Guide : BeginLatex
    //
    //  Then the region is passed to the filter using the
    //  SetExtractionRegion() method.
    //
    //  \index{itk::ExtractImageFilter!SetExtractionRegion()}
    //
    //  Software Guide : EndLatex
  
    // Software Guide : BeginCodeSnippet
    extractFilter->SetExtractionRegion( desiredRegion );
    // Software Guide : EndCodeSnippet
    // Software Guide : BeginCodeSnippet
    typedef itk::PasteImageFilter< MiddleImageType, OutputImageType > PasteFilterType;
    PasteFilterType::Pointer pasteFilter = PasteFilterType::New();
    // Software Guide : EndCodeSnippet
    // Software Guide : BeginCodeSnippet
    typedef itk::MedianImageFilter< MiddleImageType, MiddleImageType > MedianFilterType;
    MedianFilterType::Pointer medianFilter = MedianFilterType::New();
    // 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
    extractFilter->SetInput( inputImage );
    medianFilter->SetInput( extractFilter->GetOutput() );
    pasteFilter->SetSourceImage( medianFilter->GetOutput() );
    pasteFilter->SetDestinationImage( inputImage );
    pasteFilter->SetDestinationIndex( start );
    MiddleImageType::SizeType indexRadius;
    indexRadius[0] = 1; // radius along x
    indexRadius[1] = 1; // radius along y
    indexRadius[2] = 0; // radius along z
    medianFilter->SetRadius( indexRadius );
    medianFilter->UpdateLargestPossibleRegion();
    const MiddleImageType * medianImage = medianFilter->GetOutput();
    pasteFilter->SetSourceRegion( medianImage->GetBufferedRegion() );
    writer->SetInput( pasteFilter->GetOutput() );
    // Software Guide : EndCodeSnippet
  
    //  Software Guide : BeginLatex
    //
    //  Finally we execute the pipeline by invoking 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
  
    return EXIT_SUCCESS;
  }
  