InteractiveIntegral (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- mpicbg.spim.segmentation.InteractiveIntegral

All Implemented Interfaces:

ij.plugin.PlugIn
```
public class InteractiveIntegral
extends Object
implements ij.plugin.PlugIn
```
An interactive tool for determining the required radius and peak threshold

Author:

Stephan Preibisch

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`protected class`	`InteractiveIntegral.EnableListener`
`protected class`	`InteractiveIntegral.FinishButtonListener`
`protected class`	`InteractiveIntegral.FrameListener`
`protected class`	`InteractiveIntegral.ImagePlusListener`
`protected class`	`InteractiveIntegral.MaxListener`
`protected class`	`InteractiveIntegral.MinListener`
`protected class`	`InteractiveIntegral.Radius1Listener`
`protected class`	`InteractiveIntegral.Radius2Listener`
`protected class`	`InteractiveIntegral.ThresholdListener`
`static class`	`InteractiveIntegral.ValueChange`

Constructor Summary

Constructors
Constructor and Description

InteractiveIntegral()

InteractiveIntegral(ij.ImagePlus imp)

InteractiveIntegral(ij.ImagePlus imp, int channel)

Constructors
Constructor and Description
`InteractiveIntegral()`
`InteractiveIntegral(ij.ImagePlus imp)`
`InteractiveIntegral(ij.ImagePlus imp, int channel)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected void`	`close(Frame parent, SliceObserver sliceObserver, ij.ImagePlus imp)`
`static void`	`computeDifferencOfMeanSlice(Image<LongType> integralImg, Image<FloatType> sliceImg, int z, int sx1, int sy1, int sz1, int sx2, int sy2, int sz2, float min, float max)`
`Image<LongType>`	`computeIntegralImage(Image<FloatType> img)`
`static int`	`computeRadius2(int radius1)`
`protected static int`	`computeScrollbarPositionFromValue(float radius, float min, float max, int scrollbarSize)`
`protected static float`	`computeValueFromScrollbarPosition(int scrollbarPosition, float min, float max, int scrollbarSize)`
`static Image<FloatType>`	`convertToFloat(ij.ImagePlus imp, int channel, int timepoint)` Normalize and make a copy of the `ImagePlus` into an `Image`>FloatType< for faster access when copying the slices
`protected void`	`displaySliders()` Instantiates the panel for adjusting the paramters
`static ArrayList<SimplePeak>`	`findPeaks(Image<FloatType> laPlace, float minValue)`
`Image<FloatType>`	`getConvertedImage()`
`boolean`	`getLookForMaxima()`
`boolean`	`getLookForMinima()`
`int`	`getRadius1()`
`int`	`getRadius2()`
`boolean`	`getRadius2WasAdjusted()`
`double`	`getThreshold()`
`boolean`	`isFinished()`
`protected static DifferenceOfGaussian.SpecialPoint`	`isSpecialPoint(LocalNeighborhoodCursor<FloatType> neighborhoodCursor, float centerValue)`
`static void`	`main(String[] args)`
`void`	`run(String arg)`
`void`	`setInitialRadii(int r1, int r2)`
`void`	`setInitialRadius(int r1)`
`void`	`setLookForMaxima(boolean lookForMaxima)`
`void`	`setLookForMinima(boolean lookForMinima)`
`void`	`setMaxIntensityImage(double max)`
`void`	`setMinIntensityImage(double min)`
`void`	`setRadiusMax(int radiusMax)`
`void`	`setThreshold(float value)`
`protected void`	`updatePreview(InteractiveIntegral.ValueChange change)` Updates the Preview with the current parameters (radius, threshold, roi, slicenumber)
`boolean`	`wasCanceld()`

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

Constructor Detail

InteractiveIntegral

public InteractiveIntegral(ij.ImagePlus imp,
                           int channel)

InteractiveIntegral

public InteractiveIntegral(ij.ImagePlus imp)

InteractiveIntegral
```
public InteractiveIntegral()
```

Method Detail

isFinished
```
public boolean isFinished()
```

wasCanceld
```
public boolean wasCanceld()
```

setInitialRadii

public void setInitialRadii(int r1,
                            int r2)

setInitialRadius
```
public void setInitialRadius(int r1)
```

getRadius1
```
public int getRadius1()
```

getRadius2
```
public int getRadius2()
```

getThreshold
```
public double getThreshold()
```

setThreshold

public void setThreshold(float value)

getRadius2WasAdjusted

public boolean getRadius2WasAdjusted()

getLookForMaxima
```
public boolean getLookForMaxima()
```

getLookForMinima
```
public boolean getLookForMinima()
```

setLookForMaxima

public void setLookForMaxima(boolean lookForMaxima)

setLookForMinima

public void setLookForMinima(boolean lookForMinima)

setRadiusMax

public void setRadiusMax(int radiusMax)

getConvertedImage

public Image<FloatType> getConvertedImage()

setMinIntensityImage

public void setMinIntensityImage(double min)

setMaxIntensityImage

public void setMaxIntensityImage(double max)

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

run in interface ij.plugin.PlugIn

computeIntegralImage

public Image<LongType> computeIntegralImage(Image<FloatType> img)

computeDifferencOfMeanSlice

public static final void computeDifferencOfMeanSlice(Image<LongType> integralImg,
                                                     Image<FloatType> sliceImg,
                                                     int z,
                                                     int sx1,
                                                     int sy1,
                                                     int sz1,
                                                     int sx2,
                                                     int sy2,
                                                     int sz2,
                                                     float min,
                                                     float max)

updatePreview
```
protected void updatePreview(InteractiveIntegral.ValueChange change)
```
Updates the Preview with the current parameters (radius, threshold, roi, slicenumber)

Parameters:

change - - what did change

computeRadius2

public static int computeRadius2(int radius1)

findPeaks

public static ArrayList<SimplePeak> findPeaks(Image<FloatType> laPlace,
                                              float minValue)

isSpecialPoint

protected static final DifferenceOfGaussian.SpecialPoint isSpecialPoint(LocalNeighborhoodCursor<FloatType> neighborhoodCursor,
                                                                        float centerValue)

convertToFloat
```
public static Image<FloatType> convertToFloat(ij.ImagePlus imp,
                                              int channel,
                                              int timepoint)
```
Normalize and make a copy of the ImagePlus into an Image>FloatType< for faster access when copying the slices

Parameters:

imp - - the ImagePlus input image

Returns:

- the normalized copy [0...1]

displaySliders
```
protected void displaySliders()
```
Instantiates the panel for adjusting the paramters

close

protected final void close(Frame parent,
                           SliceObserver sliceObserver,
                           ij.ImagePlus imp)

computeValueFromScrollbarPosition

protected static float computeValueFromScrollbarPosition(int scrollbarPosition,
                                                         float min,
                                                         float max,
                                                         int scrollbarSize)

computeScrollbarPositionFromValue

protected static int computeScrollbarPositionFromValue(float radius,
                                                       float min,
                                                       float max,
                                                       int scrollbarSize)

main

public static void main(String[] args)

Class InteractiveIntegral

Nested Class Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

InteractiveIntegral

InteractiveIntegral

InteractiveIntegral

Method Detail

isFinished

wasCanceld

setInitialRadii

setInitialRadius

getRadius1

getRadius2

getThreshold

setThreshold

getRadius2WasAdjusted

getLookForMaxima

getLookForMinima

setLookForMaxima

setLookForMinima

setRadiusMax

getConvertedImage

setMinIntensityImage

setMaxIntensityImage

run

computeIntegralImage

computeDifferencOfMeanSlice

updatePreview

computeRadius2

findPeaks

isSpecialPoint

convertToFloat

displaySliders

close

computeValueFromScrollbarPosition

computeScrollbarPositionFromValue

main