Module org.bonej.bonej_ops

Package org.bonej.ops.mil

Class ParallelLineMIL<B extends net.imglib2.type.BooleanType<B>>

java.lang.Object

net.imagej.ops.AbstractOp

net.imagej.ops.special.AbstractUnaryOp<net.imglib2.RandomAccessibleInterval<B>,org.joml.Vector3d>

net.imagej.ops.special.AbstractBinaryOp<net.imglib2.RandomAccessibleInterval<B>,ParallelLineGenerator,org.joml.Vector3d>

net.imagej.ops.special.function.AbstractBinaryFunctionOp<net.imglib2.RandomAccessibleInterval<B>,ParallelLineGenerator,org.joml.Vector3d>

org.bonej.ops.mil.ParallelLineMIL<B>

All Implemented Interfaces:

Runnable, net.imagej.ops.Contingent, net.imagej.ops.Environmental, net.imagej.ops.Initializable, net.imagej.ops.Op, net.imagej.ops.special.BinaryInput<net.imglib2.RandomAccessibleInterval<B>,ParallelLineGenerator>, net.imagej.ops.special.BinaryOp<net.imglib2.RandomAccessibleInterval<B>,ParallelLineGenerator,org.joml.Vector3d>, net.imagej.ops.special.function.BinaryFunctionOp<net.imglib2.RandomAccessibleInterval<B>,ParallelLineGenerator,org.joml.Vector3d>, net.imagej.ops.special.function.NullaryFunctionOp<org.joml.Vector3d>, net.imagej.ops.special.function.UnaryFunctionOp<net.imglib2.RandomAccessibleInterval<B>,org.joml.Vector3d>, net.imagej.ops.special.NullaryOp<org.joml.Vector3d>, net.imagej.ops.special.Output<org.joml.Vector3d>, net.imagej.ops.special.SpecialOp, net.imagej.ops.special.UnaryInput<net.imglib2.RandomAccessibleInterval<B>>, net.imagej.ops.special.UnaryOp<net.imglib2.RandomAccessibleInterval<B>,org.joml.Vector3d>, net.imagej.ops.Threadable, org.scijava.command.Command, org.scijava.Initializable, org.scijava.plugin.SciJavaPlugin

public class ParallelLineMIL<B extends net.imglib2.type.BooleanType<B>>
extends net.imagej.ops.special.function.AbstractBinaryFunctionOp<net.imglib2.RandomAccessibleInterval<B>,ParallelLineGenerator,org.joml.Vector3d>
implements net.imagej.ops.Contingent

An op that finds the mean intercept length (MIL) vector of an interval.

A MIL vector is defined as MIL(v) = C(v) / h, where v is a set of parallel lines, C(v) is the number of times v intercept foreground, and h is the sum of lengths of v. The lines v are traced through the interval. A line intercepts foreground, when the previous point sampled along it is background, and the current one is foreground.

For example MIL vectors can be used to estimate the anisotropy of the "texture" in an image. It's best suited for images that are completely filled, and a part of a larger whole, e.g. a volume of trabecular bone.

For more details, see:

• Moreno et al., On the Efficiency of the Mean Intercept Length Tensor
• Odgaard A (1997) Three-dimensional methods for quantification of cancellous bone architecture. Bone 20: 315-28. doi:10.1016/S8756-3282(97)00007-0.
• Harrigan TP, Mann RW (1984) Characterization of microstructural anisotropy in orthotropic materials using a second rank tensor. J Mater Sci 19: 761-767. doi:10.1007/BF00540446.

Author:

Richard Domander

Nested Class Summary

Nested classes/interfaces inherited from interface net.imagej.ops.special.SpecialOp

net.imagej.ops.special.SpecialOp.Flavor

Constructor Summary

Constructors

Constructor	Description
ParallelLineMIL()

Method Summary

Modifier and Type	Method	Description
org.joml.Vector3d	calculate(net.imglib2.RandomAccessibleInterval<B> interval, ParallelLineGenerator parallelLineGenerator)	Calculates the MIL vector of the interval.
boolean	conforms()
static void	setSeed(long seed)	Sets the seed of the underlying random number generator

Methods inherited from class net.imagej.ops.special.function.AbstractBinaryFunctionOp

in1, in2, out, run, setInput1, setInput2

Methods inherited from class net.imagej.ops.AbstractOp

ops, setEnvironment

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface net.imagej.ops.special.function.BinaryFunctionOp

calculate, getIndependentInstance, run

Methods inherited from interface net.imagej.ops.special.BinaryInput

in, setInput

Methods inherited from interface net.imagej.ops.special.BinaryOp

getArity

Methods inherited from interface net.imagej.ops.Environmental

ops, setEnvironment

Methods inherited from interface net.imagej.ops.Initializable

initialize

Methods inherited from interface net.imagej.ops.special.function.NullaryFunctionOp

run

Methods inherited from interface net.imagej.ops.special.function.UnaryFunctionOp

calculate, run

Constructor Details

ParallelLineMIL

public ParallelLineMIL()

Method Details

calculate

public org.joml.Vector3d calculate(net.imglib2.RandomAccessibleInterval<B> interval,
 ParallelLineGenerator parallelLineGenerator)

Calculates the MIL vector of the interval.

Specified by:

calculate in interface net.imagej.ops.special.function.BinaryFunctionOp<net.imglib2.RandomAccessibleInterval<B extends net.imglib2.type.BooleanType<B>>,ParallelLineGenerator,org.joml.Vector3d>

Parameters:

interval - a 3D interval.

parallelLineGenerator - a generator of random lines for MIL sampling.

Returns:

a vector v parallel to the MIL lines, whose magnitude ||v|| = total length of lines / total phase changes from background to foreground

conforms

public boolean conforms()

Specified by:

conforms in interface net.imagej.ops.Contingent

setSeed

public static void setSeed(long seed)

Sets the seed of the underlying random number generator

Only affects the random offset 0 < o < increment added to the sampling points (see sampleSegment(RandomAccessible, Segment, Vector3dc, double))

Parameters:

seed - seed value