DogDetection (ImgLib2 Javadocs 0-SNAPSHOT API)

java.lang.Object
- net.imglib2.algorithm.dog.DogDetection<T>

public class DogDetection<T extends RealType<T> & NativeType<T>>
extends Object

Author:: Stephan Preibisch, Tobias Pietzsch

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class DogDetection.ExtremaType

protected class DogDetection.TypedDogDetection<F extends RealType<F> & NativeType<F>>

Nested Classes
Modifier and Type	Class and Description
`static class`	`DogDetection.ExtremaType`
`protected class`	`DogDetection.TypedDogDetection<F extends RealType<F> & NativeType<F>>`

Field Summary

Fields
Modifier and Type	Field and Description
`protected DogDetection.ExtremaType`	`extremaType`
`protected double`	`imageSigma`
`protected RandomAccessible<T>`	`input`
`protected Interval`	`interval`
`protected boolean`	`keepDoGImg`
`protected double`	`minf`
`protected double`	`minPeakValue`
`protected boolean`	`normalizeMinPeakValue`
`protected int`	`numThreads`
`protected double[]`	`pixelSize`
`protected double`	`sigmaLarger`
`protected double`	`sigmaSmaller`
`protected DogDetection.TypedDogDetection<?>`	`typedDogDetection`

Constructor Summary

Constructors
Constructor and Description
`DogDetection(RandomAccessible<T> input, Interval interval, double[] calibration, double sigmaSmaller, double sigmaLarger, DogDetection.ExtremaType extremaType, double minPeakValue, boolean normalizeMinPeakValue)` Sets up a `DogDetection` with the specified parameters (does not do any computation yet).
`DogDetection(RandomAccessible<T> input, Interval interval, double[] calibration, double sigmaSmaller, double sigmaLarger, DogDetection.ExtremaType extremaType, double minPeakValue, boolean normalizeMinPeakValue, F computationType)` Sets up a `DogDetection` with the specified parameters (does not do any computation yet).
`DogDetection(RandomAccessibleInterval<T> input, double[] calibration, double sigmaSmaller, double sigmaLarger, DogDetection.ExtremaType extremaType, double minPeakValue, boolean normalizeMinPeakValue)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`double`	`getImageSigma()`
`boolean`	`getKeepDoGImg()`
`double`	`getMinf()`
`double`	`getMinPeakValue()`
`boolean`	`getNormalizeMinPeakValue()`
`int`	`getNumThreads()`
`ArrayList<Point>`	`getPeaks()` If you want to get subpixel-localized peaks, call `getSubpixelPeaks()` directly.
`ArrayList<RefinedPeak<Point>>`	`getSubpixelPeaks()`
`void`	`setExecutorService(ExecutorService service)`
`void`	`setImageSigma(double imageSigma)`
`void`	`setKeepDoGImg(boolean keepDoGImg)`
`void`	`setMinf(double minf)`
`void`	`setMinPeakValue(double minPeakValue)`
`void`	`setNormalizeMinPeakValue(boolean normalizeMinPeakValue)`
`void`	`setNumThreads(int numThreads)`

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

- Field Detail
  - input
```
protected final RandomAccessible<T extends RealType<T> & NativeType<T>> input
```
  - interval
```
protected final Interval interval
```
  - sigmaSmaller
```
protected final double sigmaSmaller
```
  - sigmaLarger
```
protected final double sigmaLarger
```
  - pixelSize
```
protected final double[] pixelSize
```
  - typedDogDetection
```
protected final DogDetection.TypedDogDetection<?> typedDogDetection
```
  - imageSigma
```
protected double imageSigma
```
  - minf
```
protected double minf
```
  - extremaType
```
protected DogDetection.ExtremaType extremaType
```
  - minPeakValue
```
protected double minPeakValue
```
  - normalizeMinPeakValue
```
protected boolean normalizeMinPeakValue
```
  - keepDoGImg
```
protected boolean keepDoGImg
```
  - numThreads
```
protected int numThreads
```
- Constructor Detail
  - DogDetection
```
public DogDetection(RandomAccessibleInterval<T> input,
                    double[] calibration,
                    double sigmaSmaller,
                    double sigmaLarger,
                    DogDetection.ExtremaType extremaType,
                    double minPeakValue,
                    boolean normalizeMinPeakValue)
```
  - DogDetection
```
public DogDetection(RandomAccessible<T> input,
                    Interval interval,
                    double[] calibration,
                    double sigmaSmaller,
                    double sigmaLarger,
                    DogDetection.ExtremaType extremaType,
                    double minPeakValue,
                    boolean normalizeMinPeakValue)
```
    Sets up a DogDetection with the specified parameters (does not do any computation yet). If the input image is of type DoubleType, DoubleType will be used for computing the Difference-of-Gaussian. In all other cases, FloatType will be used).
    
    Parameters:
    
    input - the input image.
    
    interval - which interval of the input image to process
    
    calibration - The calibration, i.e., the voxel sizes in some unit for the input image.
    
    sigmaSmaller - sigma for the smaller scale in the same units as calibration.
    
    sigmaLarger - sigma for the larger scale in the same units as calibration.
    
    extremaType - which type of extrema (minima, maxima) to detect. Note that minima in the Difference-of-Gaussian correspond to bright blobs on dark background. Maxima correspond to dark blobs on bright background.
    
    minPeakValue - threshold value for detected extrema. Maxima below minPeakValue or minima above -minPeakValue will be disregarded.
    
    normalizeMinPeakValue - Whether the peak value should be normalized. The Difference-of-Gaussian is an approximation of the scale-normalized Laplacian-of-Gaussian, with a factor of f = sigmaSmaller / (sigmaLarger - sigmaSmaller). If normalizeMinPeakValue=true, the minPeakValue will be divided by f (which is equivalent to scaling the DoG by f).
  - DogDetection
```
public DogDetection(RandomAccessible<T> input,
                    Interval interval,
                    double[] calibration,
                    double sigmaSmaller,
                    double sigmaLarger,
                    DogDetection.ExtremaType extremaType,
                    double minPeakValue,
                    boolean normalizeMinPeakValue,
                    F computationType)
```
    Sets up a DogDetection with the specified parameters (does not do any computation yet).
    
    Parameters:
    
    input - the input image.
    
    interval - which interval of the input image to process
    
    calibration - The calibration, i.e., the voxel sizes in some unit for the input image.
    
    sigmaSmaller - sigma for the smaller scale in the same units as calibration.
    
    sigmaLarger - sigma for the larger scale in the same units as calibration.
    
    extremaType - which type of extrema (minima, maxima) to detect. Note that minima in the Difference-of-Gaussian correspond to bright blobs on dark background. Maxima correspond to dark blobs on bright background.
    
    minPeakValue - threshold value for detected extrema. Maxima below minPeakValue or minima above -minPeakValue will be disregarded.
    
    normalizeMinPeakValue - Whether the peak value should be normalized. The Difference-of-Gaussian is an approximation of the scale-normalized Laplacian-of-Gaussian, with a factor of f = sigmaSmaller / (sigmaLarger - sigmaSmaller). If normalizeMinPeakValue=true, the minPeakValue will be divided by f (which is equivalent to scaling the DoG by f).
    
    computationType - The type to use for computing the Difference-of-Gaussian.
- Method Detail
  - getPeaks
```
public ArrayList<Point> getPeaks()
```
    If you want to get subpixel-localized peaks, call getSubpixelPeaks() directly.
  - getSubpixelPeaks
```
public ArrayList<RefinedPeak<Point>> getSubpixelPeaks()
```
  - setImageSigma
```
public void setImageSigma(double imageSigma)
```
  - setMinf
```
public void setMinf(double minf)
```
  - setMinPeakValue
```
public void setMinPeakValue(double minPeakValue)
```
  - setNormalizeMinPeakValue
```
public void setNormalizeMinPeakValue(boolean normalizeMinPeakValue)
```
  - setKeepDoGImg
```
public void setKeepDoGImg(boolean keepDoGImg)
```
  - setNumThreads
```
public void setNumThreads(int numThreads)
```
  - getImageSigma
```
public double getImageSigma()
```
  - getMinf
```
public double getMinf()
```
  - getMinPeakValue
```
public double getMinPeakValue()
```
  - getNormalizeMinPeakValue
```
public boolean getNormalizeMinPeakValue()
```
  - getKeepDoGImg
```
public boolean getKeepDoGImg()
```
  - getNumThreads
```
public int getNumThreads()
```
  - setExecutorService
```
public void setExecutorService(ExecutorService service)
```

Class DogDetection<T extends RealType<T> & NativeType<T>>

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

input

interval

sigmaSmaller

sigmaLarger

pixelSize

typedDogDetection

imageSigma

minf

extremaType

minPeakValue

normalizeMinPeakValue

keepDoGImg

numThreads

Constructor Detail

DogDetection

DogDetection

DogDetection

Method Detail

getPeaks

getSubpixelPeaks

setImageSigma

setMinf

setMinPeakValue

setNormalizeMinPeakValue

setKeepDoGImg

setNumThreads

getImageSigma

getMinf

getMinPeakValue

getNormalizeMinPeakValue

getKeepDoGImg

getNumThreads

setExecutorService