Package mpicbg.stitching.fusion

Class OverlayFusion

java.lang.Object

mpicbg.stitching.fusion.OverlayFusion

public class OverlayFusion
extends Object

Constructor Summary

Constructors

Constructor	Description
OverlayFusion()

Method Summary

Modifier and Type	Method	Description
protected static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> ij.CompositeImage	createOverlay(T targetType, ij.ImagePlus imp1, ij.ImagePlus imp2, mpicbg.models.InvertibleBoundable finalModel1, mpicbg.models.InvertibleBoundable finalModel2, int dimensionality)
static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> ij.CompositeImage	createOverlay(T targetType, ArrayList<ij.ImagePlus> images, ArrayList<mpicbg.models.InvertibleBoundable> models, int dimensionality, int timepoint, net.imglib2.interpolation.InterpolatorFactory<net.imglib2.type.numeric.real.FloatType,net.imglib2.RandomAccessible<net.imglib2.type.numeric.real.FloatType>> factory)
static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> ij.ImagePlus	createReRegisteredSeries(T targetType, ij.ImagePlus imp, ArrayList<mpicbg.models.InvertibleBoundable> models, int dimensionality)
protected static <T extends net.imglib2.type.numeric.RealType<T>> void	fuseChannel(net.imglib2.img.Img<T> output, net.imglib2.RealRandomAccessible<net.imglib2.type.numeric.real.FloatType> input, double[] offset, mpicbg.models.InvertibleCoordinateTransform transform)	Fuse one slice/volume (one channel)
static ij.ImagePlus	switchZCinXYCZT(ij.ImagePlus imp)	Rearranges an ImageJ XYCZT Hyperstack into XYZCT without wasting memory for processing 3d images as a chunk, if it is already XYZCT it will shuffle it back to XYCZT
static ij.ImagePlus	switchZTinXYCZT(ij.ImagePlus imp)	Rearranges an ImageJ XYCTZ Hyperstack into XYCZT without wasting memory for processing 3d images as a chunk, if it is already XYCTZ it will shuffle it back to XYCZT

Methods inherited from class java.lang.Object

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

Constructor Details

OverlayFusion

public OverlayFusion()

Method Details

createOverlay

protected static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>>
ij.CompositeImage createOverlay(T targetType,
 ij.ImagePlus imp1,
 ij.ImagePlus imp2,
 mpicbg.models.InvertibleBoundable finalModel1,
 mpicbg.models.InvertibleBoundable finalModel2,
 int dimensionality)

createReRegisteredSeries

public static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>>
ij.ImagePlus createReRegisteredSeries(T targetType,
 ij.ImagePlus imp,
 ArrayList<mpicbg.models.InvertibleBoundable> models,
 int dimensionality)

createOverlay

public static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>>
ij.CompositeImage createOverlay(T targetType,
 ArrayList<ij.ImagePlus> images,
 ArrayList<mpicbg.models.InvertibleBoundable> models,
 int dimensionality,
 int timepoint,
 net.imglib2.interpolation.InterpolatorFactory<net.imglib2.type.numeric.real.FloatType,net.imglib2.RandomAccessible<net.imglib2.type.numeric.real.FloatType>> factory)

fuseChannel

protected static <T extends net.imglib2.type.numeric.RealType<T>>
void fuseChannel(net.imglib2.img.Img<T> output,
 net.imglib2.RealRandomAccessible<net.imglib2.type.numeric.real.FloatType> input,
 double[] offset,
 mpicbg.models.InvertibleCoordinateTransform transform)

Fuse one slice/volume (one channel)

Parameters:

output - - same the type of the ImagePlus input

input - - FloatType, because of Interpolation that needs to be done

transform - - the transformation

switchZCinXYCZT

public static ij.ImagePlus switchZCinXYCZT(ij.ImagePlus imp)

Rearranges an ImageJ XYCZT Hyperstack into XYZCT without wasting memory for processing 3d images as a chunk, if it is already XYZCT it will shuffle it back to XYCZT

Parameters:

imp - - the input ImagePlus

Returns:

- an ImagePlus which can be the same instance if the image is XYZT, XYZ, XYT or XY - otherwise a new instance containing the same processors but in the new order XYZCT

switchZTinXYCZT

public static ij.ImagePlus switchZTinXYCZT(ij.ImagePlus imp)

Rearranges an ImageJ XYCTZ Hyperstack into XYCZT without wasting memory for processing 3d images as a chunk, if it is already XYCTZ it will shuffle it back to XYCZT

Parameters:

imp - - the input ImagePlus

Returns:

- an ImagePlus which can be the same instance if the image is XYC, XYZ, XYT or XY - otherwise a new instance containing the same processors but in the new order XYZCT