Package process

Class OverlayFusion

java.lang.Object

process.OverlayFusion

public class OverlayFusion
extends Object

Field Summary

Fields

Modifier and Type	Field	Description
static boolean	useSizeOfFirstImage

Constructor Summary

Constructors

Constructor	Description
OverlayFusion()

Method Summary

Modifier and Type	Method	Description
protected static <T extends mpicbg.imglib.type.numeric.RealType<T>> ij.CompositeImage	createOverlay(T targetType, ij.ImagePlus imp1, ij.ImagePlus imp2, mpicbg.models.InvertibleBoundable finalModel1, mpicbg.models.InvertibleBoundable finalModel2, int dimensionality, int interpolation)
static <T extends mpicbg.imglib.type.numeric.RealType<T>> ij.CompositeImage	createOverlay(T targetType, ArrayList<ij.ImagePlus> images, ArrayList<mpicbg.models.InvertibleBoundable> models, int dimensionality, int timepoint, mpicbg.imglib.interpolation.InterpolatorFactory<mpicbg.imglib.type.numeric.real.FloatType> factory)
static <T extends mpicbg.imglib.type.numeric.RealType<T>> ij.ImagePlus	createReRegisteredSeries(T targetType, ij.ImagePlus imp, ArrayList<mpicbg.models.InvertibleBoundable> models, int dimensionality, String directory, int interpolation)
static void	estimateBounds(float[] offset, int[] size, int[][] imgSizes, ArrayList<mpicbg.models.InvertibleBoundable> models, int dimensionality)	Estimate the bounds of the output image.
static void	estimateBounds(float[] offset, int[] size, List<ij.ImagePlus> images, ArrayList<mpicbg.models.InvertibleBoundable> models, int dimensionality)	Estimate the bounds of the output image.
static <T extends mpicbg.imglib.type.numeric.RealType<T>> void	fuseChannel(mpicbg.imglib.image.Image<T> output, mpicbg.imglib.image.Image<mpicbg.imglib.type.numeric.real.FloatType> input, float[] offset, mpicbg.models.InvertibleCoordinateTransform transform, mpicbg.imglib.interpolation.InterpolatorFactory<mpicbg.imglib.type.numeric.real.FloatType> factory)	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

Field Details

useSizeOfFirstImage

public static boolean useSizeOfFirstImage

Constructor Details

OverlayFusion

public OverlayFusion()

Method Details

createOverlay

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

createReRegisteredSeries

public static <T extends mpicbg.imglib.type.numeric.RealType<T>>
ij.ImagePlus createReRegisteredSeries(T targetType,
 ij.ImagePlus imp,
 ArrayList<mpicbg.models.InvertibleBoundable> models,
 int dimensionality,
 String directory,
 int interpolation)

createOverlay

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

estimateBounds

public static void estimateBounds(float[] offset,
 int[] size,
 List<ij.ImagePlus> images,
 ArrayList<mpicbg.models.InvertibleBoundable> models,
 int dimensionality)

Estimate the bounds of the output image. If there are more models than images, we assume that this encodes for more timepoints. E.g. 2 Images and 10 models would mean 5 timepoints. The arrangement of the models should be as follows: image1 timepoint1 image2 timepoint1 image1 timepoint2 ... image2 timepoint5

Parameters:

offset - - the offset, will be computed

size - - the size, will be computed

images - - all imageplus in a list

models - - all models

dimensionality - - which dimensionality (2 or 3)

estimateBounds

public static void estimateBounds(float[] offset,
 int[] size,
 int[][] imgSizes,
 ArrayList<mpicbg.models.InvertibleBoundable> models,
 int dimensionality)

Estimate the bounds of the output image. If there are more models than images, we assume that this encodes for more timepoints. E.g. 2 Images and 10 models would mean 5 timepoints. The arrangement of the models should be as follows: image1 timepoint1 image2 timepoint1 image1 timepoint2 ... image2 timepoint5

Parameters:

offset - - the offset, will be computed

size - - the size, will be computed

imgSizes - - the dimensions of all input images imgSizes[ image ][ x, y, (z) ]

models - - all models

dimensionality - - which dimensionality (2 or 3)

fuseChannel

public static <T extends mpicbg.imglib.type.numeric.RealType<T>>
void fuseChannel(mpicbg.imglib.image.Image<T> output,
 mpicbg.imglib.image.Image<mpicbg.imglib.type.numeric.real.FloatType> input,
 float[] offset,
 mpicbg.models.InvertibleCoordinateTransform transform,
 mpicbg.imglib.interpolation.InterpolatorFactory<mpicbg.imglib.type.numeric.real.FloatType> factory)

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