ImageRegionIterator.cxx

See Also

ImageConstIterator

ConditionalConstIterator

ConstNeighborhoodIterator

ConstShapedNeighborhoodIterator

ConstSliceIterator

CorrespondenceDataStructureIterator

FloodFilledFunctionConditionalConstIterator

FloodFilledImageFunctionConditionalConstIterator

FloodFilledImageFunctionConditionalIterator

FloodFilledSpatialFunctionConditionalConstIterator

FloodFilledSpatialFunctionConditionalIterator

ImageConstIterator

ImageConstIteratorWithIndex

ImageIterator

ImageIteratorWithIndex

ImageLinearConstIteratorWithIndex

ImageLinearIteratorWithIndex

ImageRandomConstIteratorWithIndex

ImageRandomIteratorWithIndex

ImageRegionConstIterator

ImageRegionConstIteratorWithIndex

ImageRegionExclusionConstIteratorWithIndex

ImageRegionExclusionIteratorWithIndex

ImageRegionIterator

ImageRegionIteratorWithIndex

ImageRegionReverseConstIterator

ImageRegionReverseIterator

ImageReverseConstIterator

ImageReverseIterator

ImageSliceConstIteratorWithIndex

ImageSliceIteratorWithIndex

NeighborhoodIterator

PathConstIterator

PathIterator

ShapedNeighborhoodIterator

SliceIterator

ImageConstIteratorWithIndex

Wiki Examples:

• All Examples

• Iterate over a region of an image (without write access)

/*=========================================================================
 *
 *  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 : BeginCommandLineArgs
//     INPUTS:  {FatMRISlice.png}
//     OUTPUTS: {ImageRegionIteratorOutput.png}
//     ARGUMENTS:    20 70 210 140
//  Software Guide : EndCommandLineArgs

// Software Guide : BeginLatex
//
// \index{Iterators!speed}
// The \doxygen{ImageRegionIterator} is optimized for
// iteration speed and is the first choice for iterative, pixel-wise operations
// when location in the image is not
// important. ImageRegionIterator is the least specialized of the ITK
// image iterator classes.  It implements all of the methods described in the
// preceding section.
//
// The following example illustrates the use of
// \doxygen{ImageRegionConstIterator} and ImageRegionIterator.
// Most of the code constructs introduced apply to other ITK iterators as
// well. This simple application crops a subregion from an image by copying
// its pixel values into to a second, smaller image.
//
// \index{Iterators!and image regions}
// \index{itk::ImageRegionIterator!example of using|(}
// We begin by including the appropriate header files.
// Software Guide : EndLatex

#include "itkImage.h"
// Software Guide : BeginCodeSnippet
#include "itkImageRegionIterator.h"
// Software Guide : EndCodeSnippet
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"

int main( int argc, char *argv[] )
{
  // Verify the number of parameters on the command line.
  if ( argc < 7 )
    {
      std::cerr << "Missing parameters. " << std::endl;
      std::cerr << "Usage: " << std::endl;
      std::cerr << argv[0]
                << " inputImageFile outputImageFile startX startY sizeX sizeY"
                << std::endl;
      return -1;
    }

  // Software Guide : BeginLatex
  //
  // Next we define a pixel type and corresponding image type. ITK iterator
  // classes expect the image type as their template parameter.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  const unsigned int Dimension = 2;

  typedef unsigned char                      PixelType;
  typedef itk::Image< PixelType, Dimension > ImageType;

  typedef itk::ImageRegionConstIterator< ImageType > ConstIteratorType;
  typedef itk::ImageRegionIterator< ImageType>       IteratorType;
  // Software Guide : EndCodeSnippet

  typedef itk::ImageFileReader< ImageType > ReaderType;
  typedef itk::ImageFileWriter< ImageType > WriterType;

  // Software Guide : BeginLatex
  //
  // Information about the subregion to copy is read from the command line. The
  // subregion is defined by an \doxygen{ImageRegion} object, with a starting
  // grid index and a size (Section~\ref{sec:ImageSection}).
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  ImageType::RegionType inputRegion;

  ImageType::RegionType::IndexType inputStart;
  ImageType::RegionType::SizeType  size;

  inputStart[0] = ::atoi( argv[3] );
  inputStart[1] = ::atoi( argv[4] );

  size[0]  = ::atoi( argv[5] );
  size[1]  = ::atoi( argv[6] );

  inputRegion.SetSize( size );
  inputRegion.SetIndex( inputStart );
  // Software Guide : EndCodeSnippet


  // Software Guide : BeginLatex
  //
  // The destination region in the output image is defined using the input region
  // size, but a different start index.  The starting index for the destination
  // region is the corner of the newly generated image.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  ImageType::RegionType outputRegion;

  ImageType::RegionType::IndexType outputStart;

  outputStart[0] = 0;
  outputStart[1] = 0;

  outputRegion.SetSize( size );
  outputRegion.SetIndex( outputStart );
  // Software Guide : EndCodeSnippet


  ReaderType::Pointer reader = ReaderType::New();
  reader->SetFileName( argv[1] );
  try
    {
    reader->Update();
    }
  catch ( itk::ExceptionObject &err)
    {
    std::cerr << "ExceptionObject caught !" << std::endl;
    std::cerr << err << std::endl;
    return -1;
    }

    // Check that the region is contained within the input image.
  if ( ! reader->GetOutput()->GetRequestedRegion().IsInside( inputRegion ) )
    {
    std::cerr << "Error" << std::endl;
    std::cerr << "The region " << inputRegion << "is not contained within the input image region "
              << reader->GetOutput()->GetRequestedRegion() << std::endl;
    return -1;
    }

  // Software Guide : BeginLatex
  //
  // After reading the input image and checking that the desired subregion is,
  // in fact, contained in the input, we allocate an output image.  It is
  // fundamental to set valid values to some of the basic image information
  // during the copying process.
  // In particular, the starting index of the output region
  // is now filled up with zero values and the coordinates of the physical
  // origin are computed as a shift from the origin of the input image. This is
  // quite important since it will allow us to later
  // register the extracted region against the original image.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  ImageType::Pointer outputImage = ImageType::New();
  outputImage->SetRegions( outputRegion );
  const ImageType::SpacingType& spacing = reader->GetOutput()->GetSpacing();
  const ImageType::PointType& inputOrigin = reader->GetOutput()->GetOrigin();
  double   outputOrigin[ Dimension ];

  for(unsigned int i=0; i< Dimension; i++)
    {
    outputOrigin[i] = inputOrigin[i] + spacing[i] * inputStart[i];
    }

  outputImage->SetSpacing( spacing );
  outputImage->SetOrigin(  outputOrigin );
  outputImage->Allocate();
  // Software Guide : EndCodeSnippet


  // Software Guide : BeginLatex
  //
  // \index{Iterators!construction of} \index{Iterators!and image regions}
  // The necessary images and region definitions are now in place.  All that is
  // left to do is to create the iterators and perform the copy.  Note that image
  // iterators are not accessed via smart pointers so they are light-weight
  // objects that are instantiated on the stack.  Also notice how the input and
  // output iterators are defined over the \emph{same corresponding region}.  Though the
  // images are different sizes, they both contain the same target subregion.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  ConstIteratorType inputIt(   reader->GetOutput(), inputRegion  );
  IteratorType      outputIt(  outputImage,         outputRegion );

  inputIt.GoToBegin();
  outputIt.GoToBegin();

  while( !inputIt.IsAtEnd() )
    {
    outputIt.Set(  inputIt.Get()  );
    ++inputIt;
    ++outputIt;
    }
  // Software Guide : EndCodeSnippet


  // Software Guide : BeginLatex
  //
  // \index{Iterators!image dimensionality}
  //  The \code{while} loop above is a common construct in ITK.  The beauty of
  //  these four lines of code is that they are equally valid for one, two,
  //  three, or even ten dimensional data, and no knowledge of the size of the
  //  image is necessary.  Consider the ugly alternative of ten nested
  //  \code{for} loops for traversing an image.
  //
  // Software Guide : EndLatex

  WriterType::Pointer writer = WriterType::New();
  writer->SetFileName( argv[2] );
  writer->SetInput( outputImage );

  try
    {
    writer->Update();
    }
  catch ( itk::ExceptionObject &err)
    {
    std::cerr << "ExceptionObject caught !" << std::endl;
    std::cerr << err << std::endl;
    return -1;
    }

  // Software Guide : BeginLatex
  //
  // Let's run this example on the image \code{FatMRISlice.png} found
  // in \code{Examples/Data}.  The command line arguments specify the
  // input and output file names, then the $x$, $y$ origin and the $x$, $y$ size
  // of the cropped subregion.
  //
  // \small
  // \begin{verbatim}
  // ImageRegionIterator FatMRISlice.png ImageRegionIteratorOutput.png 20 70 210 140
  // \end{verbatim}
  // \normalsize
  //
  // The output is the cropped subregion shown in
  // Figure~\ref{fig:ImageRegionIteratorOutput}.
  //
  // \begin{figure}
  // \centering
  // \includegraphics[width=0.4\textwidth]{FatMRISlice.eps}
  // \includegraphics[width=0.3\textwidth]{ImageRegionIteratorOutput.eps}
  // \itkcaption[Copying an image subregion using ImageRegionIterator]{Cropping a
  // region from an image.  The original image is shown at left.  The image on
  // the right is the result of applying the ImageRegionIterator example code.}
  // \protect\label{fig:ImageRegionIteratorOutput}
  // \end{figure}
  //
  // \index{itk::ImageRegionIterator!example of using|)}
  //
  // Software Guide : EndLatex

  return 0;
}