Package net.preibisch.mvrecon.process.psf

Class PSFExtraction<T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>>

java.lang.Object

net.preibisch.mvrecon.process.psf.PSFExtraction<T>

public class PSFExtraction<T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>>
extends Object

Constructor Summary

Constructors

Constructor	Description
PSFExtraction(net.imglib2.RandomAccessible<T> img, Collection<net.imglib2.RealLocalizable> locations, T type, long[] size)
PSFExtraction(net.imglib2.RandomAccessible<T> img, Collection<net.imglib2.RealLocalizable> locations, T type, long[] size, boolean multithreaded)
PSFExtraction(net.imglib2.RandomAccessibleInterval<T> img, Collection<net.imglib2.RealLocalizable> locations, T type, long[] size)
PSFExtraction(net.imglib2.RandomAccessibleInterval<T> img, Collection<net.imglib2.RealLocalizable> locations, T type, long[] size, boolean multithreaded)
PSFExtraction(net.imglib2.RealRandomAccessible<T> img, Collection<net.imglib2.RealLocalizable> locations, T type, long[] size)
PSFExtraction(net.imglib2.RealRandomAccessible<T> img, Collection<net.imglib2.RealLocalizable> locations, T type, long[] size, boolean multithreaded)
PSFExtraction(SpimData2 data, mpicbg.spim.data.sequence.ViewId viewId, String label, boolean useCorresponding, T type, long[] size)
PSFExtraction(SpimData2 data, mpicbg.spim.data.sequence.ViewId viewId, String label, boolean useCorresponding, T type, long[] size, boolean multithreaded)

Method Summary

Modifier and Type	Method	Description
static <T extends net.imglib2.type.numeric.RealType<T>> void	extractPSFLocal(net.imglib2.RealRandomAccessible<T> img, Collection<net.imglib2.RealLocalizable> locations, net.imglib2.RandomAccessibleInterval<T> psf)	Extracts the PSF by summing up the local neighborhood of locations (most likely RANSAC correspondences)
static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> void	extractPSFMultiThreaded(net.imglib2.RealRandomAccessible<T> img, Collection<net.imglib2.RealLocalizable> locations, net.imglib2.RandomAccessibleInterval<T> psfGlobal)
static ArrayList<net.imglib2.RealLocalizable>	getPoints(SpimData2 data, mpicbg.spim.data.sequence.ViewId viewId, String label, boolean useCorresponding)
net.imglib2.img.array.ArrayImg<T,?>	getPSF()
static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> net.imglib2.img.array.ArrayImg<T,?>	getTransformedNormalizedPSF(net.imglib2.img.array.ArrayImg<T,?> psf, net.imglib2.realtransform.AffineTransform3D model)
net.imglib2.img.array.ArrayImg<T,?>	getTransformedNormalizedPSF(net.imglib2.realtransform.AffineTransform3D model)
boolean	hadDetections()
static <T extends net.imglib2.type.numeric.RealType<T>> void	normalize(net.imglib2.IterableInterval<T> img)
void	removeMinProjections()
static <T extends net.imglib2.type.numeric.RealType<T>> void	removeMinProjections(net.imglib2.img.Img<T> psf)
static <T extends net.imglib2.type.numeric.RealType<T>> void	subtractProjection(net.imglib2.RandomAccessibleInterval<T> img, net.imglib2.RandomAccessibleInterval<T> proj, int projDim)
static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> net.imglib2.img.array.ArrayImg<T,?>	transform(net.imglib2.RandomAccessibleInterval<T> image, net.imglib2.realtransform.AffineTransform3D transformIn, long[] newDim, double[] offset)
static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> net.imglib2.img.array.ArrayImg<T,?>	transformPSF(net.imglib2.RandomAccessibleInterval<T> psf, net.imglib2.realtransform.AffineTransform3D model)	Transforms the extracted PSF using the affine transformation of the corresponding view

Methods inherited from class java.lang.Object

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

Constructor Details

PSFExtraction

public PSFExtraction(net.imglib2.RealRandomAccessible<T> img,
 Collection<net.imglib2.RealLocalizable> locations,
 T type,
 long[] size,
 boolean multithreaded)

PSFExtraction

public PSFExtraction(net.imglib2.RealRandomAccessible<T> img,
 Collection<net.imglib2.RealLocalizable> locations,
 T type,
 long[] size)

PSFExtraction

public PSFExtraction(net.imglib2.RandomAccessible<T> img,
 Collection<net.imglib2.RealLocalizable> locations,
 T type,
 long[] size,
 boolean multithreaded)

PSFExtraction

public PSFExtraction(net.imglib2.RandomAccessible<T> img,
 Collection<net.imglib2.RealLocalizable> locations,
 T type,
 long[] size)

PSFExtraction

public PSFExtraction(net.imglib2.RandomAccessibleInterval<T> img,
 Collection<net.imglib2.RealLocalizable> locations,
 T type,
 long[] size,
 boolean multithreaded)

PSFExtraction

public PSFExtraction(net.imglib2.RandomAccessibleInterval<T> img,
 Collection<net.imglib2.RealLocalizable> locations,
 T type,
 long[] size)

PSFExtraction

public PSFExtraction(SpimData2 data,
 mpicbg.spim.data.sequence.ViewId viewId,
 String label,
 boolean useCorresponding,
 T type,
 long[] size,
 boolean multithreaded)

PSFExtraction

public PSFExtraction(SpimData2 data,
 mpicbg.spim.data.sequence.ViewId viewId,
 String label,
 boolean useCorresponding,
 T type,
 long[] size)

Method Details

getPoints

public static ArrayList<net.imglib2.RealLocalizable> getPoints(SpimData2 data,
 mpicbg.spim.data.sequence.ViewId viewId,
 String label,
 boolean useCorresponding)

hadDetections

public boolean hadDetections()

getPSF

public net.imglib2.img.array.ArrayImg<T,?> getPSF()

getTransformedNormalizedPSF

public net.imglib2.img.array.ArrayImg<T,?> getTransformedNormalizedPSF(net.imglib2.realtransform.AffineTransform3D model)

getTransformedNormalizedPSF

public static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>>
net.imglib2.img.array.ArrayImg<T,?> getTransformedNormalizedPSF(net.imglib2.img.array.ArrayImg<T,?> psf,
 net.imglib2.realtransform.AffineTransform3D model)

removeMinProjections

public void removeMinProjections()

removeMinProjections

public static <T extends net.imglib2.type.numeric.RealType<T>>
void removeMinProjections(net.imglib2.img.Img<T> psf)

subtractProjection

public static <T extends net.imglib2.type.numeric.RealType<T>>
void subtractProjection(net.imglib2.RandomAccessibleInterval<T> img,
 net.imglib2.RandomAccessibleInterval<T> proj,
 int projDim)

extractPSFLocal

public static <T extends net.imglib2.type.numeric.RealType<T>>
void extractPSFLocal(net.imglib2.RealRandomAccessible<T> img,
 Collection<net.imglib2.RealLocalizable> locations,
 net.imglib2.RandomAccessibleInterval<T> psf)

Extracts the PSF by summing up the local neighborhood of locations (most likely RANSAC correspondences)

Type Parameters:

T - pixel type

Parameters:

img - - the source image

locations - - the locations inside the source image

psf - - RAI to write result to

extractPSFMultiThreaded

public static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>>
void extractPSFMultiThreaded(net.imglib2.RealRandomAccessible<T> img,
 Collection<net.imglib2.RealLocalizable> locations,
 net.imglib2.RandomAccessibleInterval<T> psfGlobal)

transformPSF

public static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>>
net.imglib2.img.array.ArrayImg<T,?> transformPSF(net.imglib2.RandomAccessibleInterval<T> psf,
 net.imglib2.realtransform.AffineTransform3D model)

Transforms the extracted PSF using the affine transformation of the corresponding view

Type Parameters:

T - pixel type

Parameters:

psf - - the extracted psf (NOT z-scaling corrected)

model - - the transformation model

Returns:

the transformed psf which has odd sizes and where the center of the psf is also the center of the transformed psf

transform

public static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>>
net.imglib2.img.array.ArrayImg<T,?> transform(net.imglib2.RandomAccessibleInterval<T> image,
 net.imglib2.realtransform.AffineTransform3D transformIn,
 long[] newDim,
 double[] offset)

normalize

public static <T extends net.imglib2.type.numeric.RealType<T>>
void normalize(net.imglib2.IterableInterval<T> img)