Field Detail

• useSizeOfFirstImage

  public static boolean useSizeOfFirstImage

Constructor Detail

• OverlayFusion

  public OverlayFusion()

Method Detail

• createOverlay

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

• createReRegisteredSeries

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

• createOverlay

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

• estimateBounds

  public static void estimateBounds(float[] offset,
                                    int[] size,
                                    List<ij.ImagePlus> images,
                                    ArrayList<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<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 RealType<T>> void fuseChannel(Image<T> output,
                                                         Image<FloatType> input,
                                                         float[] offset,
                                                         InvertibleCoordinateTransform transform,
                                                         InterpolatorFactory<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