Package net.preibisch.mvrecon.process.psf

Class PSFCombination

java.lang.Object

net.preibisch.mvrecon.process.psf.PSFCombination

public class PSFCombination
extends Object

Constructor Summary

Constructors

Constructor	Description
PSFCombination()

Method Summary

Modifier and Type	Method	Description
static <T extends net.imglib2.type.Type<T>> long[]	commonSize(List<net.imglib2.img.Img<T>> images)	Returns the bounding box so that all images can fit in there or null if input is null or input.size is 0
static <T extends net.imglib2.type.numeric.RealType<T>> net.imglib2.img.Img<T>	computeAverageImage(Collection<? extends net.imglib2.RandomAccessibleInterval<T>> imgs, net.imglib2.img.ImgFactory<T> imgFactory, boolean max)	compute the average psf in original calibration and after applying the transformations
static <T extends net.imglib2.type.numeric.RealType<T>> net.imglib2.img.Img<T>	computeMaxAverageTransformedPSF(Collection<? extends net.imglib2.RandomAccessibleInterval<T>> imgs, net.imglib2.img.ImgFactory<T> imgFactory)
static long[]	computeMaxDimTransformedPSF(Collection<? extends net.imglib2.Interval> imgs)
static <S extends net.imglib2.type.numeric.RealType<S>> net.imglib2.img.Img<S>	computeMaxProjection(net.imglib2.RandomAccessibleInterval<S> avgPSF, net.imglib2.img.ImgFactory<S> factory, int minDim, boolean max)
static <T extends net.imglib2.type.numeric.RealType<T>> net.imglib2.img.Img<T>	computeMaxProjectionPSF(net.imglib2.img.Img<T> avg)
static long[]	computeMinDimTransformedPSF(Collection<? extends net.imglib2.Interval> imgs)
static <S extends net.imglib2.type.numeric.RealType<S>> net.imglib2.img.Img<S>	computeProjection(net.imglib2.img.Img<S> avgPSF, int minDim, boolean max)	Get projection along the smallest dimension (which is usually the rotation axis)
static <T extends net.imglib2.type.numeric.RealType<T>> net.imglib2.img.Img<T>	makeSameSize(net.imglib2.img.Img<T> img, long[] sizeIn)	Make image the same size as defined, center it

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

PSFCombination

public PSFCombination()

Method Details

computeMaxAverageTransformedPSF

public static <T extends net.imglib2.type.numeric.RealType<T>>
net.imglib2.img.Img<T> computeMaxAverageTransformedPSF(Collection<? extends net.imglib2.RandomAccessibleInterval<T>> imgs,
 net.imglib2.img.ImgFactory<T> imgFactory)

computeMaxProjectionPSF

public static <T extends net.imglib2.type.numeric.RealType<T>>
net.imglib2.img.Img<T> computeMaxProjectionPSF(net.imglib2.img.Img<T> avg)

computeAverageImage

public static <T extends net.imglib2.type.numeric.RealType<T>>
net.imglib2.img.Img<T> computeAverageImage(Collection<? extends net.imglib2.RandomAccessibleInterval<T>> imgs,
 net.imglib2.img.ImgFactory<T> imgFactory,
 boolean max)

compute the average psf in original calibration and after applying the transformations

Type Parameters:

T - pixel type

Parameters:

imgs - - the input images

imgFactory - - the image factory for the average image

max - - if true, use the maximal size of all inputs, otherwise the minimal size of all inputs

Returns:

averaged image

computeMaxDimTransformedPSF

public static long[] computeMaxDimTransformedPSF(Collection<? extends net.imglib2.Interval> imgs)

Parameters:

imgs - image dimensions

Returns:

- maximal dimensions of the transformed PSFs

computeMinDimTransformedPSF

public static long[] computeMinDimTransformedPSF(Collection<? extends net.imglib2.Interval> imgs)

Parameters:

imgs - image dimensions

Returns:

- maximal dimensions of the transformed PSFs

makeSameSize

public static <T extends net.imglib2.type.numeric.RealType<T>>
net.imglib2.img.Img<T> makeSameSize(net.imglib2.img.Img<T> img,
 long[] sizeIn)

Make image the same size as defined, center it

Type Parameters:

T - pixel type

Parameters:

img - input image

sizeIn - the size we want

Returns:

centered image of same type

computeProjection

public static <S extends net.imglib2.type.numeric.RealType<S>>
net.imglib2.img.Img<S> computeProjection(net.imglib2.img.Img<S> avgPSF,
 int minDim,
 boolean max)

Get projection along the smallest dimension (which is usually the rotation axis)

Type Parameters:

S - pixel type

Parameters:

avgPSF - - the average psf

minDim - - along which dimension to project, if set to <0, the smallest dimension will be chosen

max - - if true max projection, else min projection

Returns:

- the averaged, projected PSF

computeMaxProjection

public static <S extends net.imglib2.type.numeric.RealType<S>>
net.imglib2.img.Img<S> computeMaxProjection(net.imglib2.RandomAccessibleInterval<S> avgPSF,
 net.imglib2.img.ImgFactory<S> factory,
 int minDim,
 boolean max)

commonSize

public static <T extends net.imglib2.type.Type<T>>
long[] commonSize(List<net.imglib2.img.Img<T>> images)

Returns the bounding box so that all images can fit in there or null if input is null or input.size is 0

Type Parameters:

T - pixel type

Parameters:

images - input images

Returns:

largest size in every dimension or null