Constructor Detail

• PairWiseStitchingImgLib

  public PairWiseStitchingImgLib()

Method Detail

• stitchPairwise

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

• performStitching

  public static <T extends RealType<T>,S extends RealType<S>> PairWiseStitchingResult performStitching(Image<T> img1,
                                                                                                       Image<S> img2,
                                                                                                       StitchingParameters params)

• computePhaseCorrelation

  public static <T extends RealType<T>,S extends RealType<S>> PairWiseStitchingResult computePhaseCorrelation(Image<T> img1,
                                                                                                              Image<S> img2,
                                                                                                              int numPeaks,
                                                                                                              boolean subpixelAccuracy)

• getImage

  public static <T extends RealType<T>> Image<T> getImage(ij.ImagePlus imp,
                                                          Roi roi,
                                                          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 RealType<T>> boolean averageAllChannels(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 RealType<T>> boolean fillInChannel(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 RealType<T>,S extends RealType<S>> void averageAllChannels(Image<T> target,
                                                                                         ArrayList<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

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

  sources - - a list of input Images

• getWrappedImageUnsignedByte

  public static Image<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 Image<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 Image<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,
                                          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 Roi getOnlyRectangularRoi(Roi roi)