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.
   *
   *=========================================================================*/
  #if defined(_MSC_VER)
  #pragma warning ( disable : 4786 )
  #endif
  
  //  Software Guide : BeginLatex
  //
  //  This example illustrates the common task of extracting a 2D slice from a
  //  3D volume. This is typically used for display purposes and for expediting
  //  user feedback in interactive programs. Here we simply read a 3D volume,
  //  extract one of its slices and save it as a 2D image. Note that caution
  //  should be used when working with 2D slices from a 3D dataset, since for
  //  most image processing operations, the application of a filter on a
  //  extracted slice is not equivalent to first applying the filter in the
  //  volume and then extracting the slice.
  //
  //  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 $(N-1)$-dimensional images from $N$-dimensional
  //  ones.
  //
  //  \index{itk::ExtractImageFilter!header}
  //
  //  Software Guide : EndLatex
  
  // Software Guide : BeginCodeSnippet
  #include "itkExtractImageFilter.h"
  // Software Guide : EndCodeSnippet
  
  
  #include "itkImage.h"
  
  
  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  output2DImageFile " << 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 $2D$.
    //
    //  Software Guide : EndLatex
  
    // Software Guide : BeginCodeSnippet
    typedef signed short        InputPixelType;
    typedef signed short        OutputPixelType;
  
    typedef itk::Image< InputPixelType,  3 >    InputImageType;
    typedef itk::Image< OutputPixelType, 2 >    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, OutputImageType > FilterType;
    FilterType::Pointer filter = FilterType::New();
    filter->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 $0$ in one dimension.  This will indicate to
    //  ExtractImageFilter that a dimensional reduction has been
    //  specified. Here we take the region from the largest possible 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();
    InputImageType::RegionType inputRegion =
             reader->GetOutput()->GetLargestPossibleRegion();
    // 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 $0$. This will indicate to the
    //  ExtractImageFilter that the output image should have a
    //  dimension less than the input image.
    //
    //  Software Guide : EndLatex
  
    // Software Guide : BeginCodeSnippet
    InputImageType::SizeType size = inputRegion.GetSize();
    size[2] = 0;
    // 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]=0;}.
    //
    //  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
    filter->SetExtractionRegion( desiredRegion );
    // 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
    filter->SetInput( reader->GetOutput() );
    writer->SetInput( filter->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;
  }
  