EulerCorrection (ImageJ2 Javadocs 0-SNAPSHOT API)

java.lang.Object
- net.imagej.ops.AbstractOp
- - net.imagej.ops.special.AbstractUnaryOp<I,O>
 - - net.imagej.ops.special.hybrid.AbstractUnaryHybridC<I,O>
 - - net.imagej.ops.special.hybrid.AbstractUnaryHybridCF<RandomAccessibleInterval,DoubleType>
 - net.imagej.ops.topology.eulerCharacteristic.EulerCorrection

All Implemented Interfaces:

Runnable, Contingent, Environmental, Initializable, Op, Ops.Topology.EulerCorrection, NullaryComputerOp<DoubleType>, UnaryComputerOp<RandomAccessibleInterval,DoubleType>, NullaryFunctionOp<DoubleType>, UnaryFunctionOp<RandomAccessibleInterval,DoubleType>, NullaryHybridCF<DoubleType>, UnaryHybridCF<RandomAccessibleInterval,DoubleType>, NullaryOp<DoubleType>, NullaryOutputFactory<DoubleType>, Output<DoubleType>, OutputMutable<DoubleType>, SpecialOp, UnaryInput<RandomAccessibleInterval>, UnaryOp<RandomAccessibleInterval,DoubleType>, UnaryOutputFactory<RandomAccessibleInterval,DoubleType>, Threadable, Command, SciJavaPlugin
```
public class EulerCorrection>
extends AbstractUnaryHybridCF<RandomAccessibleInterval,DoubleType>
implements Ops.Topology.EulerCorrection, Contingent
```
An Op which calculates the correction needed to approximate the contribution of the image to the Euler characteristic χ of the whole image. That is, it's assumed that the image is a small part cut from a larger sample.
From Odgaard & Gundersen (see below): "-- the Euler characteristic of the entire 3-D space will not be obtained by simply adding the Euler characteristics of cubic specimens. By doing this, the contribution of the lower dimensional elements will not be considered". They give the correction as c = -1/2χ_2 - 1/4χ_1 - -1/8χ_0, where
- χ_2 = χ of all the faces of the stack
- χ_1 = χ of all the edges of the stack
- χ_0 = χ of all the corner vertices of the stack.
Each face contributes to two, each edge to four, and each corner to eight stacks.
Odgaard A, Gundersen HJG (1993)
Quantification of connectivity in cancellous bone, with special emphasis on 3-D reconstructions.
Bone 14: 173-182.
doi:10.1016/8756-3282(93)90245-6
Author:

Michael Doube (Royal Veterinary College, London), Richard Domander (Royal Veterinary College, London) NB: Methods are public and static to help testing

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class EulerCorrection.Traverser>
A convenience class for passing parameters
- Nested classes/interfaces inherited from interface net.imagej.ops.special.SpecialOp
 SpecialOp.Flavor

Nested Classes
Modifier and Type	Class and Description
`static class`	`EulerCorrection.Traverser<B extends BooleanType<B>>` A convenience class for passing parameters

Field Summary
- Fields inherited from interface net.imagej.ops.Ops.Topology.EulerCorrection
  NAME

Constructor Summary

Constructors
Constructor and Description

EulerCorrection()

Constructors
Constructor and Description
`EulerCorrection()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`compute(RandomAccessibleInterval<B> interval, DoubleType output)` Computes the output given some input.
`boolean`	`conforms()` The algorithm is defined only for 3D images
`DoubleType`	`createOutput(RandomAccessibleInterval<B> input)` Create an output object given some input.
`static <B extends BooleanType<B>> int`	`stackCorners(EulerCorrection.Traverser<B> traverser)` Counts the foreground voxels in stack corners
`static <B extends BooleanType<B>> long`	`stackEdges(EulerCorrection.Traverser<B> traverser)` Count the foreground voxels on the edges lining the stack
`static <B extends BooleanType<B>> int`	`stackFaces(EulerCorrection.Traverser<B> traverser)` Count the foreground voxels on the faces that line the stack
`static <B extends BooleanType<B>> long`	`voxelEdgeFaceIntersections(EulerCorrection.Traverser<B> traverser)` Count the intersections between voxel edges in each 2x2 neighborhood and the faces lining the stack
`static <B extends BooleanType<B>> long`	`voxelEdgeIntersections(EulerCorrection.Traverser<B> traverser)` Count the number of intersections between voxels in each 2x1 neighborhood and the the edges of the stack
`static <B extends BooleanType<B>> long`	`voxelFaceIntersections(EulerCorrection.Traverser<B> traverser)` Count the intersections between voxels in each 2x2 neighborhood and the faces lining the stack

Methods inherited from class net.imagej.ops.special.hybrid.AbstractUnaryHybridC
in, out, setInput, setOutput

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 java.lang.Runnable
run

Methods inherited from interface net.imagej.ops.Environmental
ops, setEnvironment

Methods inherited from interface net.imagej.ops.special.hybrid.UnaryHybridCF
calculate, calculate, createOutput, getIndependentInstance, run, run

Methods inherited from interface net.imagej.ops.special.computer.UnaryComputerOp
compute

Methods inherited from interface net.imagej.ops.special.UnaryOp
getArity

Methods inherited from interface net.imagej.ops.special.UnaryInput
in, setInput

Methods inherited from interface net.imagej.ops.special.hybrid.NullaryHybridCF
run

Methods inherited from interface net.imagej.ops.special.OutputMutable
setOutput

Methods inherited from interface net.imagej.ops.special.SpecialOp
candidates, filterArity, op

Methods inherited from interface net.imagej.ops.Initializable
initialize

Methods inherited from interface net.imagej.ops.special.Output
out

- Constructor Detail
 - EulerCorrection
```
public EulerCorrection()
```
- Method Detail
 - conforms
```
public boolean conforms()
```
 The algorithm is defined only for 3D images
 
 Specified by:
 
 conforms in interface Contingent
 - compute
```
public void compute(RandomAccessibleInterval interval,
 DoubleType output)
```
 Description copied from interface: UnaryComputerOp
 
 Computes the output given some input.
 
 Specified by:
 
 compute in interface UnaryComputerOp<RandomAccessibleInterval>,DoubleType>
 
 Parameters:
 
 interval - Argument to the computation, which must be non-null
 
 output - Object where the computation's result will be stored, which must be non-null and a different object than input
 - createOutput
```
public DoubleType createOutput(RandomAccessibleInterval input)
```
 Description copied from interface: UnaryOutputFactory
 
 Create an output object given some input.
 
 Specified by:
 
 createOutput in interface UnaryOutputFactory<RandomAccessibleInterval>,DoubleType>
 
 Parameters:
 
 input - which determines how to create the output
 
 Returns:
 
 output, depending on the input
 - stackCorners
```
public static > int stackCorners(EulerCorrection.Traverser traverser)
```
 Counts the foreground voxels in stack corners
 Calculates χ_0 from Odgaard and Gundersen
 - stackEdges
```
public static > long stackEdges(EulerCorrection.Traverser traverser)
```
 Count the foreground voxels on the edges lining the stack
 Contributes to χ_1 from Odgaard and Gundersen
 - stackFaces
```
public static > int stackFaces(EulerCorrection.Traverser traverser)
```
 Count the foreground voxels on the faces that line the stack
 Contributes to χ_2 from Odgaard and Gundersen
 - voxelEdgeIntersections
```
public static > long voxelEdgeIntersections(EulerCorrection.Traverser traverser)
```
 Count the number of intersections between voxels in each 2x1 neighborhood and the the edges of the stack
 Contributes to χ_1 from Odgaard and Gundersen
 - voxelEdgeFaceIntersections
```
public static > long voxelEdgeFaceIntersections(EulerCorrection.Traverser traverser)
```
 Count the intersections between voxel edges in each 2x2 neighborhood and the faces lining the stack
 Contributes to χ_2 from Odgaard and Gundersen
 - voxelFaceIntersections
```
public static > long voxelFaceIntersections(EulerCorrection.Traverser traverser)
```
 Count the intersections between voxels in each 2x2 neighborhood and the faces lining the stack
 Contributes to χ_2 from Odgaard and Gundersen

Class EulerCorrection<B extends BooleanType<B>>

Nested Class Summary

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

Field Summary

Fields inherited from interface net.imagej.ops.Ops.Topology.EulerCorrection

Constructor Summary

Method Summary

Methods inherited from class net.imagej.ops.special.hybrid.AbstractUnaryHybridC

Methods inherited from class net.imagej.ops.AbstractOp

Methods inherited from class java.lang.Object

Methods inherited from interface java.lang.Runnable

Methods inherited from interface net.imagej.ops.Environmental

Methods inherited from interface net.imagej.ops.special.hybrid.UnaryHybridCF

Methods inherited from interface net.imagej.ops.special.computer.UnaryComputerOp

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

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

Methods inherited from interface net.imagej.ops.special.hybrid.NullaryHybridCF

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

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

Methods inherited from interface net.imagej.ops.Initializable

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

Constructor Detail

EulerCorrection

Method Detail

conforms

compute

createOutput

stackCorners

stackEdges

stackFaces

voxelEdgeIntersections

voxelEdgeFaceIntersections

voxelFaceIntersections