script.imglib.analysis

Class DoGPeaks<N extends RealType<N>>

java.lang.Object

java.util.AbstractCollection<E>

java.util.AbstractList<E>

java.util.ArrayList<float[]>

script.imglib.analysis.DoGPeaks<N>

All Implemented Interfaces:

Serializable, Cloneable, Iterable<float[]>, Collection<float[]>, List<float[]>, RandomAccess

public class DoGPeaks<N extends RealType<N>>
extends ArrayList<float[]>

Perform a difference of Gaussian on the given Image, and this class itself becomes the List of found peaks, each as a float[] array that specifies its position. See also DifferenceOfGaussian, DifferenceOfGaussianPeak.

See Also:

Serialized Form

Field Summary

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

Constructors

Constructor and Description
DoGPeaks(Image<N> img, double[] sigmaLarge, double[] sigmaSmall, Number minPeakValue, Number normalizationFactor)
DoGPeaks(Image<N> img, Number sigmaLarge, Number sigmaSmall, Number minPeakValue, Number normalizationFactor) Consider the as isotropic: apply the same sigma to all dimensions.
DoGPeaks(Object fn, double[] sigmaLarge, double[] sigmaSmall, Number minPeakValue, Number normalizationFactor)
DoGPeaks(Object fn, float[] sigmaLarge, float[] sigmaSmall, Number minPeakValue, Number normalizationFactor) Consider the as an isotropic image: apply the same sigma to all dimensions.
DoGPeaks(Object fn, List<Number> sigmaLarge, List<Number> sigmaSmall, Number minPeakValue, Number normalizationFactor) Consider the as an isotropic image: apply the same sigma to all dimensions.
DoGPeaks(Object fn, Number sigmaLarge, Number sigmaSmall, Number minPeakValue, Number normalizationFactor)

Method Summary

Modifier and Type	Method and Description
List<Object>	asPoints() Returns a list of peaks as Java3D points: Point2f for 2D images, Point3f for 3D images, and Point4f for 4D images.
List<Object>	asPoints(float[] scalingFactor) Returns a list of peaks as Java3D points if possible: Point2f for 2D images Point3f for 3D images Point4f for 4D images
List<Object>	asPoints(Number scalingFactor) Returns a list of peaks as Java3D points: Point2f for 2D images, Point3f for 3D images, and Point4f for 4D images.
List<DifferenceOfGaussianPeak<FloatType>>	getPeaks() Get all peaks as DifferenceOfGaussianPeak instances.

Methods inherited from class java.util.ArrayList

add, add, addAll, addAll, clear, clone, contains, ensureCapacity, forEach, get, indexOf, isEmpty, iterator, lastIndexOf, listIterator, listIterator, remove, remove, removeAll, removeIf, removeRange, replaceAll, retainAll, set, size, sort, spliterator, subList, toArray, toArray, trimToSize

Methods inherited from class java.util.AbstractList

equals, hashCode

Methods inherited from class java.util.AbstractCollection

containsAll, toString

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.List

containsAll, equals, hashCode

Methods inherited from interface java.util.Collection

parallelStream, stream

Constructor Detail

DoGPeaks

public DoGPeaks(Object fn,
                Number sigmaLarge,
                Number sigmaSmall,
                Number minPeakValue,
                Number normalizationFactor)
         throws Exception

Throws:

Exception

DoGPeaks

public DoGPeaks(Image<N> img,
                Number sigmaLarge,
                Number sigmaSmall,
                Number minPeakValue,
                Number normalizationFactor)
         throws Exception

Consider the as isotropic: apply the same sigma to all dimensions.

Throws:

Exception

DoGPeaks

public DoGPeaks(Object fn,
                List<Number> sigmaLarge,
                List<Number> sigmaSmall,
                Number minPeakValue,
                Number normalizationFactor)
         throws Exception

Consider the as an isotropic image: apply the same sigma to all dimensions.

Throws:

Exception

DoGPeaks

public DoGPeaks(Object fn,
                float[] sigmaLarge,
                float[] sigmaSmall,
                Number minPeakValue,
                Number normalizationFactor)
         throws Exception

Consider the as an isotropic image: apply the same sigma to all dimensions.

Throws:

Exception

DoGPeaks

public DoGPeaks(Object fn,
                double[] sigmaLarge,
                double[] sigmaSmall,
                Number minPeakValue,
                Number normalizationFactor)
         throws Exception

Throws:

Exception

DoGPeaks

public DoGPeaks(Image<N> img,
                double[] sigmaLarge,
                double[] sigmaSmall,
                Number minPeakValue,
                Number normalizationFactor)
         throws Exception

Parameters:

img - The Image to search peaks into.

sigmaLarge - A double[] array with a sigma value for each dimension of the image.

sigmaSmall - A double[] array with a sigma value for each dimension of the image.

minPeakValue - The lowest intensity value for a difference of Gaussian peak to be considered so.

normalizationFactor - See DifferenceOfGaussian.

Throws:

Exception

Method Detail

getPeaks

public List<DifferenceOfGaussianPeak<FloatType>> getPeaks()

Get all peaks as DifferenceOfGaussianPeak instances.

asPoints

public List<Object> asPoints(float[] scalingFactor)
                      throws Exception

Returns a list of peaks as Java3D points if possible: Point2f for 2D images Point3f for 3D images Point4f for 4D images

Throws:

IllegalArgumentException - if scalingFactor.length is different than the image dimensions.

Exception - if the image dimensions is not 2, 3, or 4.

asPoints

public List<Object> asPoints()
                      throws Exception

Returns a list of peaks as Java3D points: Point2f for 2D images, Point3f for 3D images, and Point4f for 4D images. For images of 1D or more than 4D, returns a list of float[].

Throws:

Exception

asPoints

public List<Object> asPoints(Number scalingFactor)
                      throws Exception

Returns a list of peaks as Java3D points: Point2f for 2D images, Point3f for 3D images, and Point4f for 4D images. For images of 1D or more than 4D, returns a list of float[].

Throws:

Exception