InteractiveDoG (Fiji Javadocs 0-SNAPSHOT API)

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

All Implemented Interfaces:

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

Author:

Stephan Preibisch

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`protected class`	`InteractiveDoG.ApplyButtonListener`
`protected class`	`InteractiveDoG.EnableListener`
`protected class`	`InteractiveDoG.FinishedButtonListener`
`protected class`	`InteractiveDoG.FrameListener`
`protected class`	`InteractiveDoG.ImagePlusListener`
`protected class`	`InteractiveDoG.MaxListener`
`protected class`	`InteractiveDoG.MinListener`
`protected class`	`InteractiveDoG.RoiListener` Tests whether the ROI was changed and will recompute the preview
`protected class`	`InteractiveDoG.Sigma2Listener`
`protected class`	`InteractiveDoG.SigmaListener`
`protected class`	`InteractiveDoG.ThresholdListener`
`static class`	`InteractiveDoG.ValueChange`

Field Summary

Fields
Modifier and Type Field and Description

Rectangle standardRectangle

static int standardSensitivity

Fields
Modifier and Type	Field and Description
`Rectangle`	`standardRectangle`
`static int`	`standardSensitivity`

Constructor Summary

Constructors
Constructor and Description

InteractiveDoG()

InteractiveDoG(ij.ImagePlus imp)

InteractiveDoG(ij.ImagePlus imp, int channel)

Constructors
Constructor and Description
`InteractiveDoG()`
`InteractiveDoG(ij.ImagePlus imp)`
`InteractiveDoG(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, InteractiveDoG.RoiListener roiListener)`
`protected static int`	`computeScrollbarPositionFromValue(float sigma, float min, float max, int scrollbarSize)`
`static float`	`computeSigma2(float sigma1, int sensitivity)`
`protected static float`	`computeValueFromScrollbarPosition(int scrollbarPosition, float min, float max, int scrollbarSize)`
`static FloatImagePlus<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
`static FloatImagePlus<FloatType>`	`convertToFloat(ij.ImagePlus imp, int channel, int timepoint, double min, double max)`
`static FloatImagePlus<FloatType>`	`createImgLib2(List<float[]> img, int w, int h)`
`protected void`	`displaySliders()` Instantiates the panel for adjusting the paramters
`protected Image<FloatType>`	`extractImage(FloatImagePlus<FloatType> source, Rectangle rectangle, int extraSize)` Extract the current 2d region of interest from the souce image
`FloatImagePlus<FloatType>`	`getConvertedImage()`
`double`	`getInitialSigma()`
`boolean`	`getLookForMaxima()`
`boolean`	`getLookForMinima()`
`double`	`getSigma2()`
`boolean`	`getSigma2WasAdjusted()`
`double`	`getThreshold()`
`boolean`	`isFinished()`
`static void`	`main(String[] args)`
`void`	`run(String arg)`
`void`	`setInitialSigma(float value)`
`void`	`setLookForMaxima(boolean lookForMaxima)`
`void`	`setLookForMinima(boolean lookForMinima)`
`void`	`setMaxIntensityImage(double max)`
`void`	`setMinIntensityImage(double min)`
`void`	`setSigma2isAdjustable(boolean state)`
`void`	`setSigmaMax(float sigmaMax)`
`void`	`setThreshold(float value)`
`protected void`	`updatePreview(InteractiveDoG.ValueChange change)` Updates the Preview with the current parameters (sigma, threshold, roi, slicenumber)
`boolean`	`wasCanceled()`

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

Field Detail

standardSensitivity
```
public static int standardSensitivity
```

standardRectangle
```
public Rectangle standardRectangle
```

Constructor Detail

InteractiveDoG

public InteractiveDoG(ij.ImagePlus imp,
                      int channel)

InteractiveDoG

public InteractiveDoG(ij.ImagePlus imp)

InteractiveDoG
```
public InteractiveDoG()
```

Method Detail

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

wasCanceled
```
public boolean wasCanceled()
```

getInitialSigma
```
public double getInitialSigma()
```

setInitialSigma

public void setInitialSigma(float value)

getSigma2
```
public double getSigma2()
```

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

setThreshold

public void setThreshold(float value)

getSigma2WasAdjusted
```
public boolean getSigma2WasAdjusted()
```

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

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

setLookForMaxima

public void setLookForMaxima(boolean lookForMaxima)

setLookForMinima

public void setLookForMinima(boolean lookForMinima)

setSigmaMax

public void setSigmaMax(float sigmaMax)

setSigma2isAdjustable

public void setSigma2isAdjustable(boolean state)

getConvertedImage

public FloatImagePlus<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

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

Parameters:

change - - what did change

computeSigma2

public static float computeSigma2(float sigma1,
                                  int sensitivity)

extractImage
```
protected Image<FloatType> extractImage(FloatImagePlus<FloatType> source,
                                        Rectangle rectangle,
                                        int extraSize)
```
Extract the current 2d region of interest from the souce image

Parameters:

source - - the source image, a Image which is a copy of the ImagePlus

rectangle - - the area of interest

extraSize - - the extra size around so that detections at the border of the roi are not messed up

Returns:

convertToFloat

public static FloatImagePlus<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]

convertToFloat

public static FloatImagePlus<FloatType> convertToFloat(ij.ImagePlus imp,
                                                       int channel,
                                                       int timepoint,
                                                       double min,
                                                       double max)

createImgLib2

public static FloatImagePlus<FloatType> createImgLib2(List<float[]> img,
                                                      int w,
                                                      int h)

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

close

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

computeValueFromScrollbarPosition

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

computeScrollbarPositionFromValue

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

main

public static void main(String[] args)

Class InteractiveDoG

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

standardSensitivity

standardRectangle

Constructor Detail

InteractiveDoG

InteractiveDoG

InteractiveDoG

Method Detail

isFinished

wasCanceled

getInitialSigma

setInitialSigma

getSigma2

getThreshold

setThreshold

getSigma2WasAdjusted

getLookForMaxima

getLookForMinima

setLookForMaxima

setLookForMinima

setSigmaMax

setSigma2isAdjustable

getConvertedImage

setMinIntensityImage

setMaxIntensityImage

run

updatePreview

computeSigma2

extractImage

convertToFloat

convertToFloat

createImgLib2

displaySliders

close

computeValueFromScrollbarPosition

computeScrollbarPositionFromValue

main