Iterators/ShapedNeighborhoodIterators1.cxx

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 *  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.
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 *         http://www.apache.org/licenses/LICENSE-2.0.txt
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 *  distributed under the License is distributed on an "AS IS" BASIS,
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 *  See the License for the specific language governing permissions and
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 *=========================================================================*/

#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkNeighborhoodAlgorithm.h"
#include <math.h>

// Software Guide : BeginLatex
//
// This example uses \doxygen{ShapedNeighborhoodIterator} to implement a binary
// erosion algorithm.  If we think of an image $I$ as a set of pixel indices,
// then erosion of $I$ by a smaller set $E$, called the \emph{structuring
// element}, is the set of all indices at locations $x$ in $I$ such that when
// $E$ is positioned at $x$, every element in $E$ is also contained in $I$.
//
// This type of algorithm is easy to implement with shaped neighborhood
// iterators because we can use the iterator itself as the structuring element
// $E$ and move it sequentially through all positions $x$.  The result at $x$
// is obtained by checking values in a simple iteration loop through the
// neighborhood stencil.
//
// We need two iterators, a shaped iterator for the input image and a regular
// image iterator for writing results to the output image.
//
// Software Guide : EndLatex

// Software Guide : BeginCodeSnippet
#include "itkConstShapedNeighborhoodIterator.h"
#include "itkImageRegionIterator.h"
// Software Guide : EndCodeSnippet

int main( int argc, char ** argv )
{
  if ( argc < 4 )
    {
    std::cerr << "Missing parameters. " << std::endl;
    std::cerr << "Usage: " << std::endl;
    std::cerr << argv[0]
              << " inputImageFile outputImageFile element_radius"
              << std::endl;
    return -1;
    }

  // Software Guide : BeginLatex
  //
  // Since we are working with binary images in this example, an \code{unsigned
  // char} pixel type will do.  The image and iterator types are defined using
  // the pixel type.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  typedef unsigned char               PixelType;
  typedef itk::Image< PixelType, 2 >  ImageType;

  typedef itk::ConstShapedNeighborhoodIterator<
                                          ImageType
                                            > ShapedNeighborhoodIteratorType;

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

  typedef itk::ImageFileReader< ImageType > ReaderType;
  ReaderType::Pointer reader = ReaderType::New();
  reader->SetFileName( argv[1] );

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

  ImageType::Pointer output = ImageType::New();
  output->SetRegions(reader->GetOutput()->GetRequestedRegion());
  output->Allocate();

  // Software Guide : BeginLatex
  //
  // Refer to the examples in Section~\ref{sec:itkNeighborhoodIterator} or the
  // source code of this example for a description of how to read the input image
  // and allocate a matching output image.
  //
  // The size of the structuring element is read from the command line and used
  // to define a radius for the shaped neighborhood iterator.  Using the method
  // developed in section~\ref{sec:itkNeighborhoodIterator} to minimize bounds
  // checking, the iterator itself is not initialized until entering the
  // main processing loop.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  unsigned int element_radius = ::atoi( argv[3] );
  ShapedNeighborhoodIteratorType::RadiusType radius;
  radius.Fill(element_radius);
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // The face calculator object introduced in
  // Section~\ref{sec:NeighborhoodExample3} is created and used as before.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  typedef itk::NeighborhoodAlgorithm::ImageBoundaryFacesCalculator<
                                                ImageType > FaceCalculatorType;

  FaceCalculatorType faceCalculator;
  FaceCalculatorType::FaceListType faceList;
  FaceCalculatorType::FaceListType::iterator fit;

  faceList = faceCalculator( reader->GetOutput(),
                             output->GetRequestedRegion(),
                             radius );
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // Now we initialize some variables and constants.
  //
  // Software Guide : EndLatex


  // Software Guide : BeginCodeSnippet
  IteratorType out;

  const PixelType background_value = 0;
  const PixelType foreground_value = 255;
  const float rad = static_cast<float>(element_radius);
  // Software Guide : EndCodeSnippet


  // Software Guide : BeginLatex
  //
  // The outer loop of the algorithm is structured as in previous neighborhood
  // iterator examples.  Each region in the face list is processed in turn.  As each new
  // region is processed, the input and output iterators are initialized on that
  // region.
  //
  // The shaped iterator that ranges over the input is our structuring element
  // and its active stencil must be created accordingly.  For this example, the
  // structuring element is shaped like a circle of radius
  // \code{element\_radius}.  Each of the appropriate neighborhood offsets is
  // activated in the double \code{for} loop.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  for ( fit=faceList.begin(); fit != faceList.end(); ++fit)
    {
    ShapedNeighborhoodIteratorType it( radius, reader->GetOutput(), *fit );
    out = IteratorType( output, *fit );

    // Creates a circular structuring element by activating all the pixels less
    // than radius distance from the center of the neighborhood.

    for (float y = -rad; y <= rad; y++)
      {
      for (float x = -rad; x <= rad; x++)
        {
        ShapedNeighborhoodIteratorType::OffsetType off;

        float dis = std::sqrt( x*x + y*y );
        if (dis <= rad)
          {
          off[0] = static_cast<int>(x);
          off[1] = static_cast<int>(y);
          it.ActivateOffset(off);
          }
        }
      }
    // Software Guide : EndCodeSnippet

    // Software Guide : BeginLatex
    //
    // The inner loop, which implements the erosion algorithm, is fairly simple.
    // The \code{for} loop steps the input and output iterators through their
    // respective images.  At each step, the active stencil of the shaped iterator
    // is traversed to determine whether all pixels underneath the stencil contain
    // the foreground value, i.e. are contained within the set $I$.  Note the use
    // of the stencil iterator, \code{ci}, in performing this check.
    //
    // Software Guide : EndLatex

    // Software Guide : BeginCodeSnippet

    // Implements erosion
    for (it.GoToBegin(), out.GoToBegin(); !it.IsAtEnd(); ++it, ++out)
      {
      ShapedNeighborhoodIteratorType::ConstIterator ci;

      bool flag = true;
      for (ci = it.Begin(); ci != it.End(); ci++)
        {
        if (ci.Get() == background_value)
          {
          flag = false;
          break;
          }
        }
      if (flag == true)
        {
        out.Set(foreground_value);
        }
      else
        {
        out.Set(background_value);
        }
      }
    }
  // Software Guide : EndCodeSnippet

  typedef itk::ImageFileWriter< ImageType > WriterType;

  WriterType::Pointer writer = WriterType::New();
  writer->SetFileName( argv[2] );
  writer->SetInput( output );
  try
    {
    writer->Update();
    }
  catch ( itk::ExceptionObject &err)
    {
    std::cout << "ExceptionObject caught !" << std::endl;
    std::cout << err << std::endl;
    return -1;
    }

  return 0;
}