ImageJVirtualStack (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- ij.ImageStack
- - ij.VirtualStack
  - - mpicbg.imglib.image.display.imagej.ImageJVirtualStack<T>

public class ImageJVirtualStack<T extends Type<T>>
extends ij.VirtualStack

TODO

Author:: Stephan Preibisch, Stephan Saalfeld

Constructor Summary

Constructors
Constructor and Description
`ImageJVirtualStack(Image<T> img, int[] dim, int[] dimensionPositions)` Constructs a virtual stack of type ImageJFunctions.GRAY32 of up to 3 arbitrary dimensions Image img - the image int[] dim - which dimensions to display, can be up to three, but at least one.
`ImageJVirtualStack(Image<T> img, int type, int[] dim, int[] dimensionPositions)` Constructs a virtual stack of up to 3 arbitrary dimensions Image img - the image int type - the type of the Virtual Stack (ImageJFunctions.GRAY8, ImageJFunctions.GRAY32 or ImageJFunctions.COLOR_RGB) int[] dim - which dimensions to display, can be up to three, but at least one.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
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.
`static <T extends Type<T>> byte[]`	`extractSliceByte(Image<T> img, Display<T> display, int dimX, int dimY, int[] dimensionPositions)`
`static <T extends Type<T>> float[]`	`extractSliceFloat(Image<T> img, Display<T> display, int dimX, int dimY, int[] dimensionPositions)`
`static <T extends Type<T>> int[]`	`extractSliceRGB(Image<T> img, Display<T> display, int dimX, int dimY, int[] dimensionPositions)`
`int`	`getBitDepth()`
`String`	`getDirectory()`
`String`	`getFileName(int n)`
`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.
`int`	`getSize()`
`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.
`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`	`setBitDepth(int bitDepth)`
`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.VirtualStack
addSlice, addSlice, getProperties, saveChanges, setIndexes, size, sortDicom, translate

Methods inherited from class ij.ImageStack
addSlice, convertToFloat, create, create, crop, drawSphere, duplicate, getColorModel, getHeight, getRoi, getVoxel, getVoxels, getVoxels, getWidth, isHSB32, isLab, setColorModel, setProcessor, setRoi, setVoxel, setVoxels, setVoxels

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - ImageJVirtualStack
```
public ImageJVirtualStack(Image<T> img,
                          int type,
                          int[] dim,
                          int[] dimensionPositions)
```
    Constructs a virtual stack of up to 3 arbitrary dimensions Image img - the image int type - the type of the Virtual Stack (ImageJFunctions.GRAY8, ImageJFunctions.GRAY32 or ImageJFunctions.COLOR_RGB) int[] dim - which dimensions to display, can be up to three, but at least one. However the array has to always have a size of 3. int[] dimensionPositions - the positions inside all dimensions that might be untouched
  - ImageJVirtualStack
```
public ImageJVirtualStack(Image<T> img,
                          int[] dim,
                          int[] dimensionPositions)
```
    Constructs a virtual stack of type ImageJFunctions.GRAY32 of up to 3 arbitrary dimensions Image img - the image int[] dim - which dimensions to display, can be up to three, but at least one. However the array has to always have a size of 3. int[] dimensionPositions - the positions inside all dimensions that might be untouched
- Method Detail
  - 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.VirtualStack
  - extractSliceFloat
```
public static <T extends Type<T>> float[] extractSliceFloat(Image<T> img,
                                                            Display<T> display,
                                                            int dimX,
                                                            int dimY,
                                                            int[] dimensionPositions)
```
  - extractSliceRGB
```
public static <T extends Type<T>> int[] extractSliceRGB(Image<T> img,
                                                        Display<T> display,
                                                        int dimX,
                                                        int dimY,
                                                        int[] dimensionPositions)
```
  - extractSliceByte
```
public static <T extends Type<T>> byte[] extractSliceByte(Image<T> img,
                                                          Display<T> display,
                                                          int dimX,
                                                          int dimY,
                                                          int[] dimensionPositions)
```
  - 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.VirtualStack
  - 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.VirtualStack
  - deleteSlice
```
public void deleteSlice(int n)
```
    Deletes the specified slice, where 1<=n<=nslices.
    
    Overrides:
    
    deleteSlice in class ij.VirtualStack
  - deleteLastSlice
```
public void deleteLastSlice()
```
    Deletes the last slice in the stack.
    
    Overrides:
    
    deleteLastSlice in class ij.VirtualStack
  - 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.VirtualStack
  - 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.VirtualStack
  - 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.VirtualStack
  - 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.VirtualStack
  - 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.VirtualStack
  - 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.VirtualStack
  - trim
```
public void trim()
```
    Frees memory by deleting a few slices from the end of the stack.
    
    Overrides:
    
    trim in class ij.VirtualStack
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class ij.ImageStack
  - getSize
```
public int getSize()
```
    Overrides:
    
    getSize in class ij.VirtualStack
  - setBitDepth
```
public void setBitDepth(int bitDepth)
```
    Overrides:
    
    setBitDepth in class ij.VirtualStack
  - getBitDepth
```
public int getBitDepth()
```
    Overrides:
    
    getBitDepth in class ij.VirtualStack
  - getDirectory
```
public String getDirectory()
```
    Overrides:
    
    getDirectory in class ij.VirtualStack
  - getFileName
```
public String getFileName(int n)
```
    Overrides:
    
    getFileName in class ij.VirtualStack

Class ImageJVirtualStack<T extends Type<T>>

Constructor Summary

Method Summary

Methods inherited from class ij.VirtualStack

Methods inherited from class ij.ImageStack

Methods inherited from class java.lang.Object

Constructor Detail

ImageJVirtualStack

ImageJVirtualStack

Method Detail

getProcessor

extractSliceFloat

extractSliceRGB

extractSliceByte

addUnsignedShortSlice

addSlice

addSlice

deleteSlice

deleteLastSlice

update

getPixels

setPixels

getImageArray

getSliceLabels

getSliceLabel

getShortSliceLabel

setSliceLabel

isRGB

isHSB

isVirtual

trim

toString

getSize

setBitDepth

getBitDepth

getDirectory

getFileName