Constructor Detail

• SpotIconGrabber

  public SpotIconGrabber(ImgPlus<T> img)

Method Detail

• getImageString

  public String getImageString(Spot spot,
                               double radiusFactor)

  Returns the image string for the specified spot. The spot x,y,z and radius coordinates are used to get a location on the image given at construction. Physical coordinates are transformed in pixel coordinates thanks to the calibration stored in the ImgPlus.

  Parameters:

  spot - the spot to generate a thumbnail image from.

  radiusFactor - a factor that determines the size of the thumbnail. The thumbnail will have a size equal to the spot diameter times this radius.

• grabImage

  public final Img<T> grabImage(long x,
                                long y,
                                long slice,
                                long width,
                                long height)

  Returns a 2D slice extract around the specified coordinates.

  Parameters:

  x - top-left x coordinate.

  y - top-left y coordinate.

  slice - z-slice index.

  width - width of the extract.

  height - height of the extract.

  Returns:

  a new Img containing the extract, potentially padded with 0s.

• grabImage

  public final Img<T> grabImage(long x,
                                long y,
                                long slice,
                                long width,
                                long height,
                                long depth)

  Returns a 3D cropped copy around the specified coordinates.

  Parameters:

  x - top-left x coordinate.

  y - top left y coordinate.

  slice - central z-slice index.

  width - width of the extract.

  height - height of the extract.

  depth - depth (along z) of the extract.

  Returns:

  a new Img containing the extract, potentially padded with 0s.