Field Detail

• redrawDelay

  public static long redrawDelay

Constructor Detail

• Fusion

  public Fusion()

Method Detail

• fuse

  public static <T extends RealType<T> & NativeType<T>> ij.ImagePlus fuse(T targetType,
                                                                          ArrayList<ij.ImagePlus> images,
                                                                          ArrayList<InvertibleBoundable> models,
                                                                          int dimensionality,
                                                                          boolean subpixelResolution,
                                                                          int fusionType,
                                                                          String outputDirectory,
                                                                          boolean noOverlap,
                                                                          boolean ignoreZeroValues,
                                                                          boolean displayImages)

  Parameters:

  targetType -

  images -

  models -

  dimensionality -

  subpixelResolution - - if there is no subpixel resolution, we do not need to convert to float as no interpolation is necessary, we can compute everything with RealType

• fuseBlock

  protected static <T extends RealType<T>> void fuseBlock(Img<T> output,
                                                          ArrayList<? extends ImageInterpolation<? extends RealType<?>>> input,
                                                          double[] offset,
                                                          ArrayList<InvertibleBoundable> transform,
                                                          PixelFusion fusion,
                                                          boolean displayFusion)

  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

• fuseBlockNoOverlap

  protected static <T extends RealType<T>> void fuseBlockNoOverlap(Img<T> output,
                                                                   ArrayList<? extends ImageInterpolation<? extends RealType<?>>> input,
                                                                   double[] offset,
                                                                   ArrayList<InvertibleBoundable> transform,
                                                                   boolean displayFusion)

  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

• writeBlock

  protected static <T extends RealType<T>> void writeBlock(Img<T> outputSlice,
                                                           int numSlices,
                                                           int t,
                                                           int numTimePoints,
                                                           int c,
                                                           int numChannels,
                                                           ArrayList<? extends ImageInterpolation<? extends RealType<?>>> input,
                                                           double[] offset,
                                                           ArrayList<InvertibleBoundable> transform,
                                                           PixelFusion fusion,
                                                           String outputDirectory)

  Fuse one slice/volume (one channel)

  Parameters:

  outputSlice - - same the type of the ImagePlus input, just one slice which will be written to the output directory

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

  transform - - the transformation

• estimateBounds

  public static void estimateBounds(double[] 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(double[] 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)

• main

  public static void main(String[] args)