ITK/Examples

These are fully independent, compilable examples. There is significant overlap in the examples, but they are each intended to illustrate a different concept and be fully stand alone compilable. Please add examples in your areas of expertise! You can checkout the entire set of examples from this repository: http://gitorious.org/itkwikiexamples/itkwikiexamples

git clone git://gitorious.org/itkwikiexamples/itkwikiexamples.git ITKWikiExamples

About the Examples

• Official announcement

ItkVtkGlue

ITK and VTK are very separate toolkits - ITK for image processing and VTK for data visualization. It is often convenient to use the two together - namely, to display an ITK image on the screen. The ItkVtkGlue kit serves exactly this purpose. Also provided inside ItkVtkGlue is a QuickView class to allow a 2 line display of an ITK image.

If you download the entire ITK Wiki Examples Collection, the ItkVtkGlue directory will be included and configured. If you wish to just build a few examples, then you will need to download ItkVtkGlue and build it.

Information for Wiki Examples Users

If you just want to use the Wiki Examples, go here. You will learn how to search for examples, build a few examples and build all of the examples.

Information for Wiki Examples Developers

If you want to contribute examples go here. You will learn how to add a new example and the guidelines for writing an example.

Information for Wiki Examples Administrators

If you are a Wiki Example Administrator or want to learn more about the process go here. You will learn how the Wiki Examples repository is organized, how the repository is synced to the wiki and how to add new topics, tests and regression baselines.

Simple Operations

Example Name	ITK Classes Demonstrated	Description
Get the width and height of an image
Variable length vector	VariableLengthVector
Translate an image	TranslationTransform, ResampleImageFilter
Get some basic information about a type	NumericTraits
Apply a color map to an image	ScalarToRGBColormapImageFilter
Catch an ITK exception		Try/Catch blocks
Get the points on a Bresenham line between two points	BresenhamLine
Add an offset to a pixel index	Offset
Distance between two points	Point
Distance between two indices	Point, Index
Create a vector	Vector
Get the name/type/class of an object		GetNameOfClass()
An object which holds the index of a pixel	Index
An object which holds the size of an image	Size
An object which holds the index (start) and size of a region of an image	ImageRegion
Make part of an image transparent	RGBAPixel	Transparency, RGBA, alpha
Determine if one region is fully inside another region	ImageRegion	Region intersection, IsInside()
Determine if a pixel is inside of a region	ImageRegion	IsInside()
Determine the overlap of two regions	ImageRegion	Region intersection
Duplicate an image	ImageDuplicator
Produce an image of noise	RandomImageSource
Set specified pixels to specified values	Image

Mathematical Operations

Example Name	ITK Classes Demonstrated	Description
Create a covariant vector	CovariantVector	This is the object which should be used to represent a mathematical vector.
Compute the norm of a covariant vector	CovariantVector	In-place and non-inplace norms.
Matrix	Matrix
Mathematical constant pi = 3.14	Math
Dot product (inner product) of two vectors	Vector

Image Functions

Example Name	ITK Classes Demonstrated	Description
GuassianBlurImageFunction	GuassianBlurImageFunction

Point Set

Example Name	ITK Classes Demonstrated	Description
Create a PointSet	PointSet
Read a PointSet	PointSet
Write a PointSet	PointSet
Get the bounding box of a PointSet	PointSet

Input/Output (IO)

Example Name	ITK Classes Demonstrated	Description
Read an image file with an unknown number of components	ImageFileReader,VectorImage
Convert a C-style array to an itkImage	ImportImageFilter
Read an image file without knowing its type before hand	ImageFileReader
Write an image	ImageFileWriter
Read an image	ImageFileReader
Write a TIFF image	TIFFImageIO	This is a general demonstration of how to use a specific writer rather than relying on the ImageFileWriter to choose for you.
Display an ITK image	ImageToVTKImageFilter
Write a transform to a file	TransformFileWriter
Read a transform from a file	TransformFileReader
Create a 3D volume from a series of 2D images	ImageSeriesReader	Uses NumericSeriesFileNames to generate a list of file names

DICOM

Example Name	ITK Classes Demonstrated	Description
Resample a DICOM series	GDCMImageIO	Resample a DICOM series with user-specified spacing.

Image Processing

Example Name	ITK Classes Demonstrated	Description
Add a constant to every pixel in an image	AddImageFilter
Subtract a constant from every pixel in an image	SubtractImageFilter
Square every pixel in an image	SquareImageFilter
Upsampling an image	BSplineInterpolateImageFunction ResampleImageFilter	Interpolate missing pixels in order to upsample an image. Note this only works on scalar images.
Flip an image over specified axes	FlipImageFilter
Apply a transformation to the magnitude of vector valued image pixels	VectorRescaleIntensityImageFilter
Apply a kernel to every pixel in an image	NeighborhoodOperatorImageFilter
Compute the Laplacian of an image	LaplacianImageFilter	Input image type must be double or float
Pad an image with a constant value	ConstantPadImageFilter
IntensityWindowingImageFilter	IntensityWindowingImageFilter	Apply a linear intensity transform from a specified input range to a specified output range.
Shrink an image	ShrinkImageFilter
Normalized correlation	NormalizedCorrelationImageFilter
Multiply every pixel in an image by a constant	MultiplyImageFilter
Compute the squared difference of corresponding pixels in two images	SquaredDifferenceImageFilter
Add a constant to every pixel without duplicating the image in memory (an accessor)	AddPixelAccessor
RegionalMaximaImageFilter	RegionalMaximaImageFilter
ValuedRegionalMaximaImageFilter	ValuedRegionalMaximaImageFilter
Pixel wise compare two input images and set the output pixel to their max	MaximumImageFilter
Pixel wise compare two input images and set the output pixel to their min	MinimumImageFilter
Binary AND two images	AndImageFilter
Binary OR two images	OrImageFilter
Binary XOR (exclusive OR) two images	XorImageFilter
Invert an image using the Binary Not operation	BinaryNotImageFilter
Compose a vector image (with 3 components) from three scalar images	ComposeImageFilter
Extract a component of an itkImage with pixels with multiple components	NthElementImageAdaptor	Use built in functionality to extract a component of an itkImage with CovariantVector components. Note this does not work for itkVectorImages - see VectorIndexSelectionCastImageFilter instead.
Present an image by first performing an operation	ImageAdaptor	A demonstration of how to present an image pixel as a function of the pixel. In this example the functionality of NthElementImageAdaptor is demonstrated.
Process the nth component/element of a vector image	NthElementImageAdaptor
Label binary regions in an image and get their properties	BinaryImageToShapeLabelMapFilter	Region bounding box, etc.
Convolve an image with a kernel	ConvolutionImageFilter	Convolution.
Assign contiguous labels to connected regions of an image	RelabelComponentImageFilter
Crop an image	CropImageFilter
Compute the absolute value of an image	AbsImageFilter	magnitude
Invert an image	InvertIntensityImageFilter
Apply a mask to an image	MaskImageFilter
Pass image pixels through a sigmoid function	SigmoidImageFilter	The qualitative description of how Alpha and Beta affect the function from the ITK Software Guide and the associated images would be nice to add to the doxygen.
Threshold an image	ThresholdImageFilter	The result is the original image but with the values below (or above) the threshold "clamped" to an output value.
Threshold an image	BinaryThresholdImageFilter	The result is a binary image (inside the threshold region or outside the threshold region).
Apply a custom operation to each pixel in an image	UnaryFunctorImageFilter	Perform a custom operation on every pixel in an image. This example rotates the vector-valued pixels by 90 degrees.
Apply a predefined operation to corresponding pixels in two images	BinaryFunctorImageFilter
Apply a custom operation to corresponding pixels in two images	BinaryFunctorImageFilter	This example computes the squared difference between corresponding pixels.
Find the minimum and maximum value (and the position of the value) in an image	MinimumMaximumImageCalculator
Add two images together	AddImageFilter
Subtract two images	SubtractImageFilter
Paste a part of one image into another image	PasteImageFilter
Stack multiple 2D images into a 3D image	TileImageFilter
Tile multiple images side by side	TileImageFilter
Multiply two images together	MultiplyImageFilter
Extract a portion of an image (region of interest)	RegionOfInterestImageFilter
Rescale the intensity values of an image to a specified range	RescaleIntensityImageFilter
Label connected components in a binary image	ConnectedComponentImageFilter
Normalize an image	NormalizeImageFilter
Cast an image from one type to another	CastImageFilter
Switch the axes of an image	PermuteAxesImageFilter
Linearly interpolate a position in an image	LinearInterpolateImageFunction
HammingWindowFunction	HammingWindowFunction

Vector Images

Example Name	ITK Classes Demonstrated	Description
Create a vector image	VectorImage	An image with an ND vector at each pixel
Create a vector image from a collection of scalar images	ComposeImageFilter
View a component of a vector image as if it were a scalar image	VectorImageToImageAdaptor
Extract a component of an itkVectorImage	VectorIndexSelectionCastImageFilter
Translate a vector image	TranslationTransform, VectorResampleImageFilter
Join images, stacking their components	JoinImageFilter
NeighborhoodIterator on a VectorImage	VectorImage NeighborhoodIterator

Iterating Over (Traversing) An Image

Example Name	ITK Classes Demonstrated	Description
Iterate over a region of an image with a shaped neighborhood	Create the shape manually ShapedNeighborhoodIterator
Iterate over a region of an image with a shaped neighborhood	Create the shape from a StructuringElement ShapedNeighborhoodIterator
Iterator over an image skipping a specified region	ImageRegionExclusionConstIteratorWithIndex
Randomly select pixels from a region of an image	ImageRandomConstIteratorWithIndex
Randomly select pixels from a region of an image without replacement	ImageRandomNonRepeatingConstIteratorWithIndex
Iterate over a line through an image	LineIterator	Walks a Bresenham line through an image (with write access)
Iterate over a line through an image without write access	LineConstIterator	Walks a Bresenham line through an image (without write access)
Iterate over the central region (non-boundary) separately from the face-regions (boundary)	ImageBoundaryFacesCalculator
Iterate over a region of an image with a neighborhood (with write access)	NeighborhoodIterator
Iterate over a region of an image with a neighborhood (without write access)	ConstNeighborhoodIterator
Iterate over a region of an image (with write access)	ImageRegionIterator
Iterate over a region of an image (without write access)	ImageRegionConstIterator
Make out of bounds pixels return a constant value	ConstantBoundaryCondition
Iterate over a region of an image with efficient access to the current index (with write access)	ImageRegionIteratorWithIndex
Iterate over a region of an image with efficient access to the current index (without write access)	ImageRegionConstIteratorWithIndex

Kernels

Example Name	ITK Classes Demonstrated	Description
Create a Gaussian kernel	GaussianOperator
Create a Gaussian derivative kernel	GaussianDerivativeOperator
Create a Laplacian kernel	LaplacianOperator
Create a derivative kernel	DerivativeOperator
Create the Sobel kernel	SobelOperator
Create a forward difference kernel	ForwardDifferenceOperator
Create a backward difference kernel	BackwardDifferenceOperator

Image Edges, Gradients, and Derivatives

Example Name	ITK Classes Demonstrated	Description
Compute the derivative of an image in a particular direction	DerivativeImageFilter
Compute the gradient of an image by convolution with the first derivative of a Gaussian	GradientRecursiveGaussianImageFilter
Find the gradient magnitude of the image first smoothed with a Gaussian kernel	GradientMagnitudeRecursiveGaussianImageFilter
Find higher derivatives of an image	RecursiveGaussianImageFilter
Extract the boundaries of connected regions in a binary image	BinaryContourImageFilter	Blob boundary, border
Extract the inner and outer boundaries of blobs in a binary image	BinaryContourImageFilter
Compute the gradient magnitude image	GradientMagnitudeImageFilter
Compute the Laplacian of an image	LaplacianRecursiveGaussianImageFilter

Smoothing

Example Name	ITK Classes Demonstrated	Description
Anti alias a binary image	AntiAliasBinaryImageFilter
Mean filter an image	MeanImageFilter	Replace each pixel by the mean of its neighborhood
Median filter an image	MedianImageFilter	Replace each pixel by the median of its neighborhood
Smooth an image with a discrete Gaussian filter	DiscreteGaussianImageFilter
Blur an image	BinomialBlurImageFilter
Bilateral filter an image	BilateralImageFilter	Edge preserving smoothing.
Smooth an image using curvature flow	CurvatureFlowImageFilterType
Gaussian smoothing that works with image adaptors	SmoothingRecursiveGaussianImageFilter

Morphology

Example Name	ITK Classes Demonstrated	Description
Erode a binary image	BinaryErodeImageFilter
Dilate a binary image	BinaryDilateImageFilter
Dilate a grayscale image	GrayscaleDilateImageFilter
Erode a grayscale image	GrayscaleErodeImageFilter
Erode a binary image using a flat (box) structuring element	FlatStructuringElement
An elliptical structuring element	BinaryBallStructuringElement

Curves

Example Name	ITK Classes Demonstrated	Description
Compute the mean distance between all points of two curves	ContourMeanDistanceImageFilter

Spectral Analysis

Example Name	ITK Classes Demonstrated	Description
Compute the FFT of an image	VnlFFTRealToComplexConjugateImageFilter
Compute the cross-correlation of two images in the Fourier domain	VnlFFTRealToComplexConjugateImageFilterVnlFFTComplexConjugateToRealImageFilter
Convert a real image and an imaginary image to a complex image	ComposeImageFilter

Utilities

Example Name	ITK Classes Demonstrated	Description
Copy a filter	Object	Copy/duplicate a filter
Cartesian to AzimuthElevation and vice-versa	AzimuthElevationToCartesianTransform
C-style array	FixedArray
Deep copy an image
Permute a sequence of indices	ImageRandomNonRepeatingConstIteratorWithIndex
Random number generator	MersenneTwisterRandomVariateGenerator
Map scalars into a jet colormap	JetColormapFunctor
Monitor a filter	SimpleFilterWatcher	See debug style information.
Time probe	TimeProbe	Compute the time between points in code.
Observe an event	Command
Vector container	VectorContainer
Bounding box	BoundingBox

Statistics

Example Name	ITK Classes Demonstrated	Description
Create a Gaussian distribution	GaussianDistribution
Create a histogram from a list of sample measurements	SampleToHistogramFilter
Create a list of sample measurements	ListSample
Create a list of samples from an image without duplicating the data	ImageToListSampleAdaptor
Create a list of samples with associated class IDs	MembershipSample
2D Gaussian Mixture Model Expectation Maximization	ExpectationMaximizationMixtureModelEstimator	EM
1D KMeans Clustering	KdTreeBasedKMeansClustering
3D KMeans Clustering	KdTreeBasedKMeansClustering
Cluster the pixels in a greyscale image	ScalarImageKmeansImageFilter

Spatial Objects

Example Name	ITK Classes Demonstrated	Description
Convert a spatial object to an image	SpatialObjectToImageFilter
Ellipse	EllipseSpatialObject
Line spatial object	LineSpatialObject, LineSpatialObjectPoint	Specify a piecewise-linear object by specifying points along the line.
Plane spatial object	PlaneSpatialObject
Blob	BlobSpatialObject

Inspection

Example Name	ITK Classes Demonstrated	Description
Combine two images by alternating blocks of a checkerboard pattern	CheckerBoardImageFilter
Printing a pixel value to the console	GetPixel

Image Registration

Example Name	ITK Classes Demonstrated	Description
A basic global registration of two images	ImageRegistrationMethod, TranslationTransform	Translation only transform.
A global registration of two images	ImageRegistrationMethod, AffineTransform	Full affine transform.
A global registration of two images	ImageRegistrationMethod, BSplineDeformableTransform	BSpline transform.
Mutual Information	MutualInformationImageToImageMetric, TranslationTransform	Global registration by maximizing the mutual information and using a translation only transform
Mutual Information Affine	MutualInformationImageToImageMetric, AffineTransform	Global registration by maximizing the mutual information and using an affine transform

Image Segmentation

Example Name	ITK Classes Demonstrated	Description
Mean shift clustering
KMeans Clustering
Multiphase Chan And Vese Sparse Field Level Set Segmentation	ScalarChanAndVeseSparseLevelSetImageFilter, ScalarChanAndVeseLevelSetFunction
Single-phase Chan And Vese Sparse Field Level Set Segmentation	ScalarChanAndVeseSparseLevelSetImageFilter, ScalarChanAndVeseLevelSetFunction
Single-phase Chan And Vese Dense Field Level Set Segmentation	ScalarChanAndVeseDenseLevelSetImageFilter, ScalarChanAndVeseLevelSetFunction

Meshes

Example Name	ITK Classes Demonstrated	Description
Decimation
Add points and edges
Compute normals of a mesh	QuadEdgeMeshNormalFilter
Planar parameterization of a mesh	ParameterizationQuadEdgeMeshFilter	Compute linear parameterization of a mesh homeomorphic to a disk on the plane

Wish List

Example Name	ITK Classes Demonstrated	Description
Compute distributions of image pixels using GMM EM	GaussianMixtureModelComponent
LevenbergMarquart
IterativeClosestPoints
MedianImageFunction	MedianImageFunction
Demonstrate all operators	NeighborhoodOperator
Color Normalized Correlation	NormalizedCorrelationImageFilter
ContourSpatialObject	ContourSpatialObject
Store non-pixel associated data in an image	MetaDataDictionary
Level Sets
Region Growing
Mesh subdivision
Separate foreground and background using Otsu's method	OtsuThresholdImageFilter
Extract contours	SimpleContourExtractorImageFilter
Present an image of RGBPixel pixels as an image of vectors	RGBToVectorImageAdaptor
HoughTransform2DCirclesImageFilter	HoughTransform2DCirclesImageFilter
HoughTransform2DLinesImageFilter	HoughTransform2DLinesImageFilter
Write data from Matlab in a format readable by ITK
Write data from ITK in a format readable by Matlab

Included in the ITK Repository

Example Name	ITK Classes Demonstrated	Description
Image registration

Matlab

Example Name	ITK Classes Demonstrated	Description

Developer Examples

Example Name	ITK Classes Demonstrated	Description
Throw an exception
Produce an image programmatically.	ImageSource	Nothing in, image out.
Filter an image	ImageToImageFilter	Image in, same type of image out.
Write a filter with multiple inputs of the same type.	ImageToImageFilter	Two images in (same type), same type of image out.
Write a filter with multiple inputs of different types.	ImageToImageFilter	Two images in (different type), image (same type as first input) out.
Write a filter with multiple outputs of the same type.	ImageToImageFilter	Images in, two images out (same type as first input).
Get or set a member variable of an ITK class.		SetMacro, GetMacro
Output an error, a warning, or debug information.		DebugMacro, ErrorMacro, WarningMacro

Problems

Small Problems

Example Name	ITK Classes Demonstrated	Description
SobelEdgeDetectionImageFilter	SobelEdgeDetectionImageFilter	NeighborIterator error?
Scale an image	ScaleTransform	No matching function call to SetTransform.
Traverse a region using a flood fill iterator	FloodFilledSpatialFunctionConditionalIterator	How to do this?
Compute the gradient of a vector image	GradientImageFilter	How to do this?
Compute distributions of image pixels using GMM EM	ExpectationMaximizationMixtureModelEstimator
Compute distributions of samples using GMM EM	ExpectationMaximizationMixtureModelEstimator	Someone please confirm that this outputs the mean and the variance (i.e. I used a standard deviation of 30 to create the samples and the second estimated parameter is near 1000 (~30^2) . Is this correct?)
Find edges in an image	CannyEdgeDetectionImageFilter	How to set a reasonable Threshold for the output edges?
Compute the histogram of an image	Statistics_1_1ImageToHistogramFilter	The last entry of the red histogram should contain several values, but it is 0?
Classifying pixels using KMeans	KmeansModelEstimator	How to apply the labels of the filter to the input image?
Basic region growing	RegionGrowImageFilter	Just getting started with demo...
Find connected components in an image	ConnectedThresholdImageFilter	Just need to finish it.
Convert an image from one type to another	ConvertPixelBuffer
Apply a function to every pixel with access to its neighborhood	NeighborhoodOperatorImageFunction
In-place filtering of an image	InPlaceImageFilter	This only works for filters which derive from itkInPlaceImageFilter
Pad an image	MirrorPadImageFilter	Not sure how to specify the final output size/extent. The documentation should be improved.
Pad an image by wrapping	WrapPadImageFilter	Not sure how to specify the final output size/extent. The documentation should be improved.
Convert a VTK image to an ITK image	VTKImageToImageFilter	Seems to expect an input image with only 1 component? (i.e. greyscale)

Big Problems

Example Name	ITK Classes Demonstrated	Description
Find the best position of the moving image in the fixed image.	MeanSquaresImageToImageMetric	Output (0,0) is incorrect.
Compute and display the gradient of an image	GradientImageFilter	Blank output.