ZPositionCorrection (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- org.janelia.thickness.plugin.ZPositionCorrection

All Implemented Interfaces:

ij.plugin.PlugIn
```
public class ZPositionCorrection
extends Object
implements ij.plugin.PlugIn
```
Author:

Philipp Hanslovsky <hanslovskyp@janelia.hhmi.org>

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static interface ZPositionCorrection.VisitorFactory

Nested Classes
Modifier and Type	Class and Description
`static interface`	`ZPositionCorrection.VisitorFactory`

Constructor Summary

Constructors
Constructor and Description

ZPositionCorrection()

Constructors
Constructor and Description
`ZPositionCorrection()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`static void`	`addVisitor(String name, Visitor visitor)`
`static void`	`addVisitor(String name, ZPositionCorrection.VisitorFactory factory)`
`static ij.process.FloatProcessor`	`calculateSimilarityMatrix(ij.ImagePlus input, int range)`
`static ij.process.FloatProcessor`	`createEmptyMatrix(int height)`
`static ij.ImageStack`	`downsampleStack(ij.ImageStack stackSource, double xyScale)`
`static <T extends RealType<T>> ij.ImageStack`	`generateStack(RealRandomAccessible<T> input, int width, int height, int size)`
`static <T extends RealType<T>> ij.ImageStack`	`generateStack(RealRandomAccessible<T> input, int width, int height, int size, double zScale)`
`static <T extends RealType<T>> RealRandomAccessible<T>`	`generateTransformed(RandomAccessibleInterval<T> input, Transform permutation, InvertibleRealTransform lut, T dummy)`
`static ij.ImagePlus`	`getFileFromOption(String path)`
`static boolean`	`invokeNCC(ij.ImagePlus input, int range, ij.process.FloatProcessor matrix)`
`static boolean`	`invokeSIFT(ij.ImagePlus input, int range, ij.process.FloatProcessor matrix)`
`static void`	`main(String[] args)`
`static ij.ImagePlus`	`normalize(ij.ImagePlus input)`
`static RandomAccessibleInterval<DoubleType>`	`normalizeAndWrap(ij.ImagePlus input)`
`void`	`run(String arg0)`
`static RandomAccessibleInterval<DoubleType>`	`wrapDouble(ij.ImagePlus input)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail
- ZPositionCorrection
```
public ZPositionCorrection()
```

Method Detail

addVisitor

public static void addVisitor(String name,
                              Visitor visitor)

addVisitor

public static void addVisitor(String name,
                              ZPositionCorrection.VisitorFactory factory)

run
```
public void run(String arg0)
```
Specified by:

run in interface ij.plugin.PlugIn

wrapDouble

public static RandomAccessibleInterval<DoubleType> wrapDouble(ij.ImagePlus input)

normalize

public static ij.ImagePlus normalize(ij.ImagePlus input)

normalizeAndWrap

public static RandomAccessibleInterval<DoubleType> normalizeAndWrap(ij.ImagePlus input)

calculateSimilarityMatrix

public static ij.process.FloatProcessor calculateSimilarityMatrix(ij.ImagePlus input,
                                                                  int range)

main

public static void main(String[] args)

invokeSIFT

public static boolean invokeSIFT(ij.ImagePlus input,
                                 int range,
                                 ij.process.FloatProcessor matrix)

invokeNCC

public static boolean invokeNCC(ij.ImagePlus input,
                                int range,
                                ij.process.FloatProcessor matrix)

downsampleStack

public static ij.ImageStack downsampleStack(ij.ImageStack stackSource,
                                            double xyScale)

createEmptyMatrix

public static ij.process.FloatProcessor createEmptyMatrix(int height)

getFileFromOption

public static ij.ImagePlus getFileFromOption(String path)

generateTransformed

public static <T extends RealType<T>> RealRandomAccessible<T> generateTransformed(RandomAccessibleInterval<T> input,
                                                                                  Transform permutation,
                                                                                  InvertibleRealTransform lut,
                                                                                  T dummy)

generateStack

public static <T extends RealType<T>> ij.ImageStack generateStack(RealRandomAccessible<T> input,
                                                                  int width,
                                                                  int height,
                                                                  int size,
                                                                  double zScale)

generateStack

public static <T extends RealType<T>> ij.ImageStack generateStack(RealRandomAccessible<T> input,
                                                                  int width,
                                                                  int height,
                                                                  int size)

Class ZPositionCorrection

Nested Class Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

ZPositionCorrection

Method Detail

addVisitor

addVisitor

run

wrapDouble

normalize

normalizeAndWrap

calculateSimilarityMatrix

main

invokeSIFT

invokeNCC

downsampleStack

createEmptyMatrix

getFileFromOption

generateTransformed

generateStack

generateStack