Field Detail

• defaultIndexChannels

  public static int defaultIndexChannels

• defaultIndexSlices

  public static int defaultIndexSlices

• defaultIndexFrames

  public static int defaultIndexFrames

• choice

  public String[] choice

Constructor Detail

• Hyperstack_rearranger

  public Hyperstack_rearranger()

Method Detail

• run

  public void run(String arg0)

  Specified by:

  run in interface ij.plugin.PlugIn

• reorderHyperstack

  public static ij.ImagePlus reorderHyperstack(ij.ImagePlus imp,
                                               String newOrder,
                                               boolean closeOldImp,
                                               boolean showNewImp)

  Creates a new Hyperstack with a different order of dimensions, the ImageProcessors are not copied but just linked from the input ImagePlus

  Parameters:

  imp - - the input ImagePlus

  newOrder - - the new order, can be "CZT", "CTZ", "ZCT", "ZTC", TCZ" or "TZC"

  closeOldImp - - close the old one?

  showNewImp - - show the new one?

  Returns:

  - a new ImagePlus with different order of Processors linked from the old ImagePlus

• reorderHyperstack

  public static ij.CompositeImage reorderHyperstack(ij.ImagePlus imp,
                                                    int targetChannels,
                                                    int targetSlices,
                                                    int targetFrames,
                                                    boolean closeOldImp,
                                                    boolean showNewImp)

  Creates a new Hyperstack with a different order of dimensions, the ImageProcessors are not copied but just linked from the input ImagePlus id's used here, reflecting (XY)CZT: channel = 0 slices = 1 frames = 2

  Parameters:

  imp - - the input ImagePlus

  targetChannels - - the new id for channel (0, 1 or 2, i.e. channels stays channels or become slices or frames)

  targetSlices - - the new id for slices (0, 1 or 2 ...)

  targetFrames - - the new id for frames (0, 1 or 2 ...)

  closeOldImp - - close the old one?

  showNewImp - - show the new one?

  Returns:

  - a new ImagePlus with different order of Processors linked from the old ImagePlus

• getImageChunk

  public static ij.ImagePlus getImageChunk(ij.ImagePlus imp,
                                           int channel,
                                           int timepoint)

  Returns an ImagePlus for a 2d or 3d stack where ImageProcessors are not copied but just added.

  Parameters:

  imp - - the input image

  channel - - which channel (first channel is 1, NOT 0)

  timepoint - - which timepoint (first timepoint is 1, NOT 0)

  Returns:

  a new ImagePlus.

• convertToHyperStack

  public static ij.ImagePlus convertToHyperStack(ij.ImagePlus imp)

  Converts this image to Hyperstack if it is RGB or 8-bit color

  Parameters:

  imp - - Inputimage

  Returns:

  the output image, might be the same