Package mpicbg.stitching

Class PairWiseStitchingImgLib

java.lang.Object

mpicbg.stitching.PairWiseStitchingImgLib

public class PairWiseStitchingImgLib
extends Object

Pairwise Stitching of two ImagePlus using ImgLib1 and PhaseCorrelation. It deals with aligning two slices (2d) or stacks (3d) having an arbitrary amount of channels. If the ImagePlus contains several time-points it will only consider the first time-point as this requires global optimization of many independent 2d/3d <-> 2d/3d alignments.

Author:

Stephan Preibisch (stephan.preibisch@gmx.de)

Constructor Summary

Constructors

Constructor	Description
PairWiseStitchingImgLib()

Method Summary

Modifier and Type	Method	Description
static <T extends mpicbg.imglib.type.numeric.RealType<T>> boolean	averageAllChannels(mpicbg.imglib.image.Image<T> target, int[] offset, ij.ImagePlus imp, int timepoint)	Averages all channels into the target image.
protected static <T extends mpicbg.imglib.type.numeric.RealType<T>, S extends mpicbg.imglib.type.numeric.RealType<S>> void	averageAllChannels(mpicbg.imglib.image.Image<T> target, ArrayList<mpicbg.imglib.image.Image<S>> sources, int[] offset)	Averages all channels into the target image.
static boolean	canWrapIntoImgLib(ij.ImagePlus imp, ij.gui.Roi roi, int channel)	Determines if this imageplus with these parameters can be wrapped directly into an Image<T>.
static <T extends mpicbg.imglib.type.numeric.RealType<T>, S extends mpicbg.imglib.type.numeric.RealType<S>> PairWiseStitchingResult	computePhaseCorrelation(mpicbg.imglib.image.Image<T> img1, mpicbg.imglib.image.Image<S> img2, int numPeaks, boolean subpixelAccuracy)
static <T extends mpicbg.imglib.type.numeric.RealType<T>> boolean	fillInChannel(mpicbg.imglib.image.Image<T> target, int[] offset, ij.ImagePlus imp, int channel, int timepoint)	Averages all channels into the target image.
static <T extends mpicbg.imglib.type.numeric.RealType<T>> mpicbg.imglib.image.Image<T>	getImage(ij.ImagePlus imp, ij.gui.Roi roi, mpicbg.imglib.image.ImageFactory<T> imgFactory, int channel, int timepoint)	return an Image<T> as input for the PhaseCorrelation.
protected static ij.gui.Roi	getOnlyRectangularRoi(ij.gui.Roi roi)
static mpicbg.imglib.image.Image<mpicbg.imglib.type.numeric.real.FloatType>	getWrappedImageFloat(ij.ImagePlus imp, int channel, int timepoint)	return an Image of FloatType as input for the PhaseCorrelation.
static mpicbg.imglib.image.Image<mpicbg.imglib.type.numeric.integer.UnsignedByteType>	getWrappedImageUnsignedByte(ij.ImagePlus imp, int channel, int timepoint)	return an Image of UnsignedByteType as input for the PhaseCorrelation.
static mpicbg.imglib.image.Image<mpicbg.imglib.type.numeric.integer.UnsignedShortType>	getWrappedImageUnsignedShort(ij.ImagePlus imp, int channel, int timepoint)	return an Image of UnsignedShortType as input for the PhaseCorrelation.
static <T extends mpicbg.imglib.type.numeric.RealType<T>, S extends mpicbg.imglib.type.numeric.RealType<S>> PairWiseStitchingResult	performStitching(mpicbg.imglib.image.Image<T> img1, mpicbg.imglib.image.Image<S> img2, StitchingParameters params)
static PairWiseStitchingResult	stitchPairwise(ij.ImagePlus imp1, ij.ImagePlus imp2, ij.gui.Roi roi1, ij.gui.Roi roi2, int timepoint1, int timepoint2, StitchingParameters params)

Methods inherited from class java.lang.Object

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

Constructor Details

PairWiseStitchingImgLib

public PairWiseStitchingImgLib()

Method Details

stitchPairwise

public static PairWiseStitchingResult stitchPairwise(ij.ImagePlus imp1,
 ij.ImagePlus imp2,
 ij.gui.Roi roi1,
 ij.gui.Roi roi2,
 int timepoint1,
 int timepoint2,
 StitchingParameters params)

performStitching

public static <T extends mpicbg.imglib.type.numeric.RealType<T>,
S extends mpicbg.imglib.type.numeric.RealType<S>>
PairWiseStitchingResult performStitching(mpicbg.imglib.image.Image<T> img1,
 mpicbg.imglib.image.Image<S> img2,
 StitchingParameters params)

computePhaseCorrelation

public static <T extends mpicbg.imglib.type.numeric.RealType<T>,
S extends mpicbg.imglib.type.numeric.RealType<S>>
PairWiseStitchingResult computePhaseCorrelation(mpicbg.imglib.image.Image<T> img1,
 mpicbg.imglib.image.Image<S> img2,
 int numPeaks,
 boolean subpixelAccuracy)

getImage

public static <T extends mpicbg.imglib.type.numeric.RealType<T>>
mpicbg.imglib.image.Image<T> getImage(ij.ImagePlus imp,
 ij.gui.Roi roi,
 mpicbg.imglib.image.ImageFactory<T> imgFactory,
 int channel,
 int timepoint)

return an Image<T> as input for the PhaseCorrelation.

Parameters:

imp - - the ImagePlus

imgFactory - - the ImageFactory defining wher to put it into

channel - - which channel (if channel=0 means average all channels)

timepoint - - which timepoint

Returns:

- the Image or null if it was not an ImagePlus.GRAY8, ImagePlus.GRAY16 or ImagePlus.GRAY32

averageAllChannels

public static <T extends mpicbg.imglib.type.numeric.RealType<T>>
boolean averageAllChannels(mpicbg.imglib.image.Image<T> target,
 int[] offset,
 ij.ImagePlus imp,
 int timepoint)

Averages all channels into the target image. The size is given by the dimensions of the target image, the offset (if applicable) is given by an extra field

Parameters:

target - - the target Image

offset - - the offset of the area (might be [0,0] or [0,0,0])

imp - - the input ImagePlus

timepoint - - for which timepoint

Returns:

true if successful, false if the ImagePlus type was unknow

fillInChannel

public static <T extends mpicbg.imglib.type.numeric.RealType<T>>
boolean fillInChannel(mpicbg.imglib.image.Image<T> target,
 int[] offset,
 ij.ImagePlus imp,
 int channel,
 int timepoint)

Averages all channels into the target image. The size is given by the dimensions of the target image, the offset (if applicable) is given by an extra field

Parameters:

target - - the target Image

offset - - the offset of the area (might be [0,0] or [0,0,0])

imp - - the input ImagePlus

timepoint - - for which timepoint

Returns:

true if successful, false if the ImagePlus type was unknow

averageAllChannels

protected static <T extends mpicbg.imglib.type.numeric.RealType<T>,
S extends mpicbg.imglib.type.numeric.RealType<S>>
void averageAllChannels(mpicbg.imglib.image.Image<T> target,
 ArrayList<mpicbg.imglib.image.Image<S>> sources,
 int[] offset)

Averages all channels into the target image. The size is given by the dimensions of the target image, the offset (if applicable) is given by an extra field

Parameters:

target - - the target Image

sources - - a list of input Images

offset - - the offset of the area (might be [0,0] or [0,0,0])

getWrappedImageUnsignedByte

public static mpicbg.imglib.image.Image<mpicbg.imglib.type.numeric.integer.UnsignedByteType> getWrappedImageUnsignedByte(ij.ImagePlus imp,
 int channel,
 int timepoint)

return an Image of UnsignedByteType as input for the PhaseCorrelation. If no rectangular roi is selected, it will only wrap the existing ImagePlus!

Parameters:

imp - - the ImagePlus

channel - - which channel (if channel=0 means average all channels)

timepoint - - which timepoint

Returns:

- the Image or null if it was not an ImagePlus.GRAY8 or if channel = 0

getWrappedImageUnsignedShort

public static mpicbg.imglib.image.Image<mpicbg.imglib.type.numeric.integer.UnsignedShortType> getWrappedImageUnsignedShort(ij.ImagePlus imp,
 int channel,
 int timepoint)

return an Image of UnsignedShortType as input for the PhaseCorrelation. If no rectangular roi is selected, it will only wrap the existing ImagePlus!

Parameters:

imp - - the ImagePlus

channel - - which channel (if channel=0 means average all channels)

timepoint - - which timepoint

Returns:

- the Image or null if it was not an ImagePlus.GRAY16 or if channel = 0

getWrappedImageFloat

public static mpicbg.imglib.image.Image<mpicbg.imglib.type.numeric.real.FloatType> getWrappedImageFloat(ij.ImagePlus imp,
 int channel,
 int timepoint)

return an Image of FloatType as input for the PhaseCorrelation. If no rectangular roi is selected, it will only wrap the existing ImagePlus!

Parameters:

imp - - the ImagePlus

channel - - which channel (if channel=0 means average all channels)

timepoint - - which timepoint

Returns:

- the Image or null if it was not an ImagePlus.GRAY32 or if channel = 0

canWrapIntoImgLib

public static boolean canWrapIntoImgLib(ij.ImagePlus imp,
 ij.gui.Roi roi,
 int channel)

Determines if this imageplus with these parameters can be wrapped directly into an Image<T>. This is important, because if we would wrap the first but not the second image, they would have different ImageFactorys

Parameters:

imp - - the ImagePlus

roi -

channel - - which channel (if channel=0 means average all channels)

Returns:

true if it can be wrapped, otherwise false

getOnlyRectangularRoi

protected static ij.gui.Roi getOnlyRectangularRoi(ij.gui.Roi roi)