fiji.stacks

Class Hyperstack_rearranger

java.lang.Object

fiji.stacks.Hyperstack_rearranger

All Implemented Interfaces:

ij.plugin.PlugIn

public class Hyperstack_rearranger
extends Object
implements ij.plugin.PlugIn

Field Summary

Fields

Modifier and Type	Field and Description
String[]	choice
static int	defaultIndexChannels
static int	defaultIndexFrames
static int	defaultIndexSlices

Constructor Summary

Constructors

Constructor and Description
Hyperstack_rearranger()

Method Summary

Modifier and Type	Method and Description
static ij.ImagePlus	convertToHyperStack(ij.ImagePlus imp) Converts this image to Hyperstack if it is RGB or 8-bit color
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.
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
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
void	run(String arg0)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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