mpicbg.imglib.image.display.imagej

Class ImageJVirtualDisplay<T extends Type<T>>

java.lang.Object

ij.ImageStack

mpicbg.imglib.image.display.imagej.ImageJVirtualDisplay<T>

public class ImageJVirtualDisplay<T extends Type<T>>
extends ij.ImageStack

TODO

Author:

Stephan Preibisch, Stephan Saalfeld

Field Summary

Fields inherited from class ij.ImageStack

cTable

Constructor Summary

Constructors

Constructor and Description
ImageJVirtualDisplay(Collection<InverseTransformDescription<T>> interpolators, int[] dimensions, int type, int[] dim, int[] dimensionPositions)

Method Summary

Modifier and Type	Method and Description
void	addSlice(String sliceLabel, ij.process.ImageProcessor ip) Adds the image in 'ip' to the end of the stack.
void	addSlice(String sliceLabel, ij.process.ImageProcessor ip, int n) Adds the image in 'ip' to the stack following slice 'n'.
void	addUnsignedShortSlice(String sliceLabel, Object pixels) Obsolete.
void	deleteLastSlice() Deletes the last slice in the stack.
void	deleteSlice(int n) Deletes the specified slice, where 1<=n<=nslices.
float[]	extractSliceFloat(int slice)
float[]	extractSliceFloatSingleThreaded(int slice)
Object[]	getImageArray() Returns the stack as an array of 1D pixel arrays.
Object	getPixels(int n) Returns the pixel array for the specified slice, where 1<=n<=nslices.
ij.process.ImageProcessor	getProcessor(int n) Returns an ImageProcessor for the specified slice, where 1<=n<=nslices.
String	getShortSliceLabel(int n) Returns a shortened version (up to the first 60 characters or first newline and suffix removed) of the label of the specified slice.
String	getSliceLabel(int n) Returns the label of the specified slice, where 1<=n<=nslices.
String[]	getSliceLabels() Returns the slice labels as an array of Strings.
Collection<InverseTransformDescription<T>>	getTransformDescription()
boolean	isHSB() Returns true if this is a 3-slice HSB stack.
boolean	isRGB() Returns true if this is a 3-slice RGB stack.
boolean	isVirtual() Returns true if this is a virtual (disk resident) stack.
void	setParent(ij.ImagePlus parent)
void	setPixels(Object pixels, int n) Assigns a pixel array to the specified slice, where 1<=n<=nslices.
void	setSliceLabel(String label, int n) Sets the label of the specified slice, where 1<=n<=nslices.
String	toString()
void	trim() Frees memory by deleting a few slices from the end of the stack.
void	update(ij.process.ImageProcessor ip) Updates this stack so its attributes, such as min, max, calibration table and color model, are the same as 'ip'.

Methods inherited from class ij.ImageStack

addSlice, addSlice, convertToFloat, create, create, crop, drawSphere, duplicate, getBitDepth, getColorModel, getHeight, getRoi, getShortSliceLabel, getSize, getVoxel, getVoxels, getVoxels, getWidth, isHSB32, isLab, setBitDepth, setColorModel, setOptions, setProcessor, setRoi, setVoxel, setVoxels, setVoxels, size

Methods inherited from class java.lang.Object

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

Constructor Detail

ImageJVirtualDisplay

public ImageJVirtualDisplay(Collection<InverseTransformDescription<T>> interpolators,
                            int[] dimensions,
                            int type,
                            int[] dim,
                            int[] dimensionPositions)

Method Detail

setParent

public void setParent(ij.ImagePlus parent)

getTransformDescription

public Collection<InverseTransformDescription<T>> getTransformDescription()

getProcessor

public ij.process.ImageProcessor getProcessor(int n)

Returns an ImageProcessor for the specified slice, where 1<=n<=nslices. Returns null if the stack is empty.

Overrides:

getProcessor in class ij.ImageStack

extractSliceFloat

public float[] extractSliceFloat(int slice)

extractSliceFloatSingleThreaded

public float[] extractSliceFloatSingleThreaded(int slice)

addUnsignedShortSlice

public void addUnsignedShortSlice(String sliceLabel,
                                  Object pixels)

Obsolete. Short images are always unsigned.

Overrides:

addUnsignedShortSlice in class ij.ImageStack

addSlice

public void addSlice(String sliceLabel,
                     ij.process.ImageProcessor ip)

Adds the image in 'ip' to the end of the stack.

Overrides:

addSlice in class ij.ImageStack

addSlice

public void addSlice(String sliceLabel,
                     ij.process.ImageProcessor ip,
                     int n)

Adds the image in 'ip' to the stack following slice 'n'. Adds the slice to the beginning of the stack if 'n' is zero.

Overrides:

addSlice in class ij.ImageStack

deleteSlice

public void deleteSlice(int n)

Deletes the specified slice, where 1<=n<=nslices.

Overrides:

deleteSlice in class ij.ImageStack

deleteLastSlice

public void deleteLastSlice()

Deletes the last slice in the stack.

Overrides:

deleteLastSlice in class ij.ImageStack

update

public void update(ij.process.ImageProcessor ip)

Updates this stack so its attributes, such as min, max, calibration table and color model, are the same as 'ip'.

Overrides:

update in class ij.ImageStack

getPixels

public Object getPixels(int n)

Returns the pixel array for the specified slice, where 1<=n<=nslices.

Overrides:

getPixels in class ij.ImageStack

setPixels

public void setPixels(Object pixels,
                      int n)

Assigns a pixel array to the specified slice, where 1<=n<=nslices.

Overrides:

setPixels in class ij.ImageStack

getImageArray

public Object[] getImageArray()

Returns the stack as an array of 1D pixel arrays. Note that the size of the returned array may be greater than the number of slices currently in the stack, with unused elements set to null.

Overrides:

getImageArray in class ij.ImageStack

getSliceLabels

public String[] getSliceLabels()

Returns the slice labels as an array of Strings. Note that the size of the returned array may be greater than the number of slices currently in the stack. Returns null if the stack is empty or the label of the first slice is null.

Overrides:

getSliceLabels in class ij.ImageStack

getSliceLabel

public String getSliceLabel(int n)

Returns the label of the specified slice, where 1<=n<=nslices. Returns null if the slice does not have a label. For DICOM and FITS stacks, labels may contain header information.

Overrides:

getSliceLabel in class ij.ImageStack

getShortSliceLabel

public String getShortSliceLabel(int n)

Returns a shortened version (up to the first 60 characters or first newline and suffix removed) of the label of the specified slice. Returns null if the slice does not have a label.

Overrides:

getShortSliceLabel in class ij.ImageStack

setSliceLabel

public void setSliceLabel(String label,
                          int n)

Sets the label of the specified slice, where 1<=n<=nslices.

Overrides:

setSliceLabel in class ij.ImageStack

isRGB

public boolean isRGB()

Returns true if this is a 3-slice RGB stack.

Overrides:

isRGB in class ij.ImageStack

isHSB

public boolean isHSB()

Returns true if this is a 3-slice HSB stack.

Overrides:

isHSB in class ij.ImageStack

isVirtual

public boolean isVirtual()

Returns true if this is a virtual (disk resident) stack. This method is overridden by the VirtualStack subclass.

Overrides:

isVirtual in class ij.ImageStack

trim

public void trim()

Frees memory by deleting a few slices from the end of the stack.

Overrides:

trim in class ij.ImageStack

toString

public String toString()

Overrides:

toString in class ij.ImageStack