Iterate Region in Image With Neighborhood

Synopsis

Iterate over a region of an image with a neighborhood (with write access).

Results

Yinyang.png

Yinyang.png In VTK Window

Output:

An extensive list of the neighborhood will be printed to the screen.

Code

C++

#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkNeighborhoodIterator.h"

#include <itkImageToVTKImageFilter.h>

#include "vtkVersion.h"
#include "vtkImageViewer.h"
#include "vtkImageMapper3D.h"
#include "vtkRenderWindowInteractor.h"
#include "vtkSmartPointer.h"
#include "vtkImageActor.h"
#include "vtkInteractorStyleImage.h"
#include "vtkRenderer.h"

int
main(int argc, char * argv[])
{
  if (argc < 2)
  {
    std::cerr << "Required: filename" << std::endl;
    return EXIT_FAILURE;
  }

  using ImageType = itk::Image<unsigned char, 2>;

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

  ImageType::Pointer image = reader->GetOutput();

  ImageType::SizeType regionSize;
  regionSize[0] = 50;
  regionSize[1] = 1;

  ImageType::IndexType regionIndex;
  regionIndex[0] = 0;
  regionIndex[1] = 0;

  ImageType::RegionType region;
  region.SetSize(regionSize);
  region.SetIndex(regionIndex);

  ImageType::SizeType radius;
  radius[0] = 1;
  radius[1] = 1;

  itk::NeighborhoodIterator<ImageType> iterator(radius, image, region);


  while (!iterator.IsAtEnd())
  {
    // Set the current pixel to white
    iterator.SetCenterPixel(255);

    for (unsigned int i = 0; i < 9; i++)
    {
      ImageType::IndexType index = iterator.GetIndex(i);
      std::cout << index[0] << " " << index[1] << std::endl;

      bool IsInBounds;
      iterator.GetPixel(i, IsInBounds);
      if (IsInBounds)
      {
        iterator.SetPixel(i, 255);
      }
    }
    ++iterator;
  }

  // Visualize
  using ConnectorType = itk::ImageToVTKImageFilter<ImageType>;
  ConnectorType::Pointer connector = ConnectorType::New();
  connector->SetInput(image);

  vtkSmartPointer<vtkImageActor> actor = vtkSmartPointer<vtkImageActor>::New();
#if VTK_MAJOR_VERSION <= 5
  actor->SetInput(connector->GetOutput());
#else
  connector->Update();
  actor->GetMapper()->SetInputData(connector->GetOutput());
#endif

  vtkSmartPointer<vtkRenderWindow> renderWindow = vtkSmartPointer<vtkRenderWindow>::New();

  vtkSmartPointer<vtkRenderWindowInteractor> interactor = vtkSmartPointer<vtkRenderWindowInteractor>::New();
  interactor->SetRenderWindow(renderWindow);

  vtkSmartPointer<vtkRenderer> renderer = vtkSmartPointer<vtkRenderer>::New();
  renderWindow->AddRenderer(renderer);

  renderer->AddActor(actor);
  renderer->ResetCamera();

  renderWindow->Render();

  vtkSmartPointer<vtkInteractorStyleImage> style = vtkSmartPointer<vtkInteractorStyleImage>::New();

  interactor->SetInteractorStyle(style);

  interactor->Start();

  return EXIT_SUCCESS;
}

Classes demonstrated

template<typename TImage, typename TBoundaryCondition = ZeroFluxNeumannBoundaryCondition<TImage>>
class NeighborhoodIterator : public itk::ConstNeighborhoodIterator<TImage, TBoundaryCondition>

Defines iteration of a local N-dimensional neighborhood of pixels across an itk::Image.

This class is a loose extension of the Standard Template Library (STL) bi-directional iterator concept to masks of pixel neighborhoods within itk::Image objects. This NeighborhoodIterator base class defines simple forward and reverse iteration of an N-dimensional neighborhood mask across an image. Elements within the mask can be accessed like elements within an array.

NeighborhoodIterators are designed to encapsulate some of the complexity of working with image neighborhoods, complexity that would otherwise have to be managed at the algorithmic level. Use NeighborhoodIterators to simplify writing algorithms that perform geometrically localized operations on images (for example, convolution and morphological operations).

To motivate the discussion of NeighborhoodIterators and their use in Itk, consider the following code that takes directional derivatives at each point in an image.

itk::NeighborhoodInnerProduct<ImageType> innerProduct;

itk::DerivativeOperator<ImageType> operator;
 operator->SetOrder(1);
 operator->SetDirection(0);
 operator->CreateDirectional();

itk::NeighborhoodIterator<ImageType>
  iterator(operator->GetRadius(), myImage, myImage->GetRequestedRegion());

iterator.SetToBegin();
while ( ! iterator.IsAtEnd() )
{
  std::cout << "Derivative at index " << iterator.GetIndex() << is <<
    innerProduct(iterator, operator) << std::endl;
  ++iterator;
}

Most of the work for the programmer in the code above is in setting up for the iteration. There are three steps. First an inner product function object is created which will be used to effect convolution with the derivative kernel. Setting up the derivative kernel, DerivativeOperator, involves setting the order and direction of the derivative. Finally, we create an iterator over the RequestedRegion of the itk::Image (see Image) using the radius of the derivative kernel as the size.

Itk iterators only loosely follow STL conventions. Notice that instead of asking myImage for myImage.begin() and myImage.end(), iterator.SetToBegin() and iterator.IsAtEnd() are called. Itk iterators are typically more complex objects than traditional, pointer-style STL iterators, and the increased overhead required to conform to the complete STL API is not always justified.

The API for creating and manipulating a NeighborhoodIterator mimics that of the itk::ImageIterators. Like the itk::ImageIterator, a ConstNeighborhoodIterator is defined on a region of interest in an itk::Image. Iteration is constrained within that region of interest.

A NeighborhoodIterator is constructed as a container of pointers (offsets) to a geometric neighborhood of image pixels. As the central pixel position in the mask is moved around the image, the neighboring pixel pointers (offsets) are moved accordingly.

A pixel neighborhood is defined as a central pixel location and an N-dimensional radius extending outward from that location.

Pixels in a neighborhood can be accessed through a NeighborhoodIterator like elements in an array. For example, a 2D neighborhood with radius 2x1 has indices:

0  1  2  3  4
5  6  7  8  9
10 11 12 13 14

Now suppose a NeighborhoodIterator with the above dimensions is constructed and positioned over a neighborhood of values in an Image:

1.2 1.3 1.8 1.4 1.1
1.8 1.1 0.7 1.0 1.0
2.1 1.9 1.7 1.4 2.0

Shown below is some sample pixel access code and the values that it returns.

SizeValueType c = (SizeValueType) (iterator.Size() / 2); // get offset of center pixel
SizeValueType s = iterator.GetStride(1);            // y-dimension step size

std::cout << iterator.GetPixel(7)      << std::endl;
std::cout << iterator.GetCenterPixel() << std::endl;
std::cout << iterator.GetPixel(c)      << std::endl;
std::cout << iterator.GetPixel(c-1)    << std::endl;
std::cout << iterator.GetPixel(c-s)    << std::endl;
std::cout << iterator.GetPixel(c-s-1)  << std::endl;
std::cout << *iterator[c]              << std::endl;

Results:

0.7
0.7
0.7
1.1
1.8
1.3
0.7

Use of GetPixel() is preferred over the *iterator[] form, and can be used without loss of efficiency in most cases. Some variations (subclasses) of NeighborhoodIterators may exist which do not support the latter API. Corresponding SetPixel() methods exist to modify pixel values in non-const NeighborhoodIterators.

NeighborhoodIterators are “bidirectional iterators”. They move only in two directions through the data set. These directions correspond to the layout of the image data in memory and not to spatial directions of the N-dimensional itk::Image. Iteration always proceeds along the fastest increasing dimension (as defined by the layout of the image data). For itk::Image this is the first dimension specified (i.e. for 3-dimensional (x,y,z) NeighborhoodIterator proceeds along the x-dimension) (For random access iteration through N-dimensional indices, use RandomAccessNeighborhoodIterator).

Each subclass of a ConstNeighborhoodIterator may also define its own mechanism for iteration through an image. In general, the Iterator does not directly keep track of its spatial location in the image, but uses a set of internal loop variables and offsets to trigger wraps at itk::Image region boundaries, and to identify the end of the itk::Image region.

See

DerivativeOperator

See

NeighborhoodInnerProduct

MORE INFORMATION

For a complete description of the ITK Image Iterators and their API, please see the Iterators chapter in the ITK Software Guide. The ITK Software Guide is available in print and as a free .pdf download from https://www.itk.org.

See

ImageConstIterator

See

ConditionalConstIterator

See

ConstNeighborhoodIterator

See

ConstShapedNeighborhoodIterator

See

ConstSliceIterator

See

CorrespondenceDataStructureIterator

See

FloodFilledFunctionConditionalConstIterator

See

FloodFilledImageFunctionConditionalConstIterator

See

FloodFilledImageFunctionConditionalIterator

See

FloodFilledSpatialFunctionConditionalConstIterator

See

FloodFilledSpatialFunctionConditionalIterator

See

ImageConstIterator

See

ImageConstIteratorWithIndex

See

ImageIterator

See

ImageIteratorWithIndex

See

ImageLinearConstIteratorWithIndex

See

ImageLinearIteratorWithIndex

See

ImageRandomConstIteratorWithIndex

See

ImageRandomIteratorWithIndex

See

ImageRegionConstIterator

See

ImageRegionConstIteratorWithIndex

See

ImageRegionExclusionConstIteratorWithIndex

See

ImageRegionExclusionIteratorWithIndex

See

ImageRegionIterator

See

ImageRegionIteratorWithIndex

See

ImageRegionReverseConstIterator

See

ImageRegionReverseIterator

See

ImageReverseConstIterator

See

ImageReverseIterator

See

ImageSliceConstIteratorWithIndex

See

ImageSliceIteratorWithIndex

See

NeighborhoodIterator

See

PathConstIterator

See

PathIterator

See

ShapedNeighborhoodIterator

See

SliceIterator

See

ImageConstIteratorWithIndex

See

ShapedImageNeighborhoodRange

ITK Sphinx Examples:

• All ITK Sphinx Examples

• Iterate Region In Image With Neighborhood

• Neighborhood Iterator On Vector Image

Subclassed by itk::ConstShapedNeighborhoodIterator< TImage, TBoundaryCondition >

See itk::NeighborhoodIterator for additional documentation.