AbstractVirtualStack (ImgLib2 Javadocs 0-SNAPSHOT API)

java.lang.Object
- ij.ImageStack
- - ij.VirtualStack
  - - net.imglib2.img.display.imagej.AbstractVirtualStack

Direct Known Subclasses:

ImageJVirtualStack, PlanarImgToVirtualStack
```
public abstract class AbstractVirtualStack
extends ij.VirtualStack
```
Abstract class to simplify the implementation of an VirtualStack.
This class is intended to be used in ImageJVirtualStack and PlanarImgToVirtualStack.

Author:

Matthias Arzt

Constructor Summary

Constructors
Constructor and Description

AbstractVirtualStack(int width, int height, int size, int bitDepth)

Constructors
Constructor and Description
`AbstractVirtualStack(int width, int height, int size, int bitDepth)`

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addSlice(ij.process.ImageProcessor ip)`
`void`	`addSlice(String name)`
`void`	`addSlice(String sliceLabel, ij.process.ImageProcessor ip)`
`void`	`addSlice(String sliceLabel, ij.process.ImageProcessor ip, int n)`
`void`	`addSlice(String sliceLabel, Object pixels)`
`void`	`addUnsignedShortSlice(String sliceLabel, Object pixels)`
`ij.ImageStack`	`convertToFloat()`
`ij.ImageStack`	`crop(int x, int y, int z, int width, int height, int depth)`
`void`	`deleteLastSlice()`
`void`	`deleteSlice(int n)`
`void`	`drawSphere(double radius, int xc, int yc, int zc)`
`ij.ImageStack`	`duplicate()`
`int`	`getBitDepth()`
`ColorModel`	`getColorModel()`
`String`	`getDirectory()`
`String`	`getFileName(int n)`
`int`	`getHeight()`
`Object[]`	`getImageArray()`
`Object`	`getPixels(int n)`
`protected abstract Object`	`getPixelsZeroBasedIndex(int index)` This method is used internally by `AbstractVirtualStack` to implement `getPixels(int)`.
`ij.process.ImageProcessor`	`getProcessor(int n)`
`Rectangle`	`getRoi()`
`String`	`getShortSliceLabel(int n)`
`int`	`getSize()`
`String`	`getSliceLabel(int n)`
`String[]`	`getSliceLabels()`
`protected RandomAccessibleInterval<?>`	`getSliceZeroBasedIndex(int index)` This method is used internally by `AbstractVirtualStack` to implement `getVoxels(int, int, int, int, int, int, float[])` and `setVoxels(int, int, int, int, int, int, float[])`.
`float[]`	`getVoxels(int x0, int y0, int z0, int w, int h, int d, float[] voxels)`
`float[]`	`getVoxels(int x0, int y0, int z0, int w, int h, int d, float[] voxels, int channel)`
`int`	`getWidth()`
`boolean`	`isHSB()`
`boolean`	`isLab()`
`boolean`	`isRGB()`
`boolean`	`isVirtual()`
`protected boolean`	`isWritable()` If this method return's false the methods `setPixels(java.lang.Object, int)` and `setVoxels(int, int, int, int, int, int, float[])` will have no effect.
`int`	`saveChanges(int n)` Currently not implemented
`void`	`setBitDepth(int bitDepth)`
`void`	`setColorModel(ColorModel cm)`
`protected void`	`setMinAndMax(double min, double max)`
`void`	`setPixels(Object pixels, int n)`
`protected abstract void`	`setPixelsZeroBasedIndex(int index, Object pixels)` This method is used internally by `AbstractVirtualStack` to implement `setPixels(java.lang.Object, int)`.
`void`	`setProcessor(ij.process.ImageProcessor ip, int n)`
`void`	`setRoi(Rectangle roi)`
`void`	`setSliceLabel(String label, int n)`
`void`	`setVoxels(int x0, int y0, int z0, int w, int h, int d, float[] voxels)`
`void`	`setVoxels(int x0, int y0, int z0, int w, int h, int d, float[] voxels, int channel)`
`int`	`size()`
`ij.ImageStack`	`sortDicom(String[] strings, String[] info, int maxDigits)`
`String`	`toString()`
`void`	`trim()`
`void`	`update(ij.process.ImageProcessor ip)`

Methods inherited from class ij.VirtualStack
getProperties, setIndexes, translate

Methods inherited from class ij.ImageStack
create, create, getVoxel, isHSB32, setVoxel

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

- Constructor Detail
  - AbstractVirtualStack
```
public AbstractVirtualStack(int width,
                            int height,
                            int size,
                            int bitDepth)
```
- Method Detail
  - setMinAndMax
```
protected void setMinAndMax(double min,
                            double max)
```
  - getPixels
```
public final Object getPixels(int n)
```
    Overrides:
    
    getPixels in class ij.VirtualStack
  - setPixels
```
public final void setPixels(Object pixels,
                            int n)
```
    Overrides:
    
    setPixels in class ij.VirtualStack
  - isWritable
```
protected boolean isWritable()
```
    If this method return's false the methods setPixels(java.lang.Object, int) and setVoxels(int, int, int, int, int, int, float[]) will have no effect.
  - getPixelsZeroBasedIndex
```
protected abstract Object getPixelsZeroBasedIndex(int index)
```
    This method is used internally by AbstractVirtualStack to implement getPixels(int).
    Returns an array that contains the pixels of the specified XY-plane. The type of the array must be byte[], short[], int[] or float[] and must match the type indicated by getBitDepth().
    
    Parameters:
    
    index - Zero based index of the plane. (Warning VirtualStack.getPixels(int) uses one base indices).
    
    See Also:
    
    ImageStack.getBitDepth()
  - setPixelsZeroBasedIndex
```
protected abstract void setPixelsZeroBasedIndex(int index,
                                                Object pixels)
```
    This method is used internally by AbstractVirtualStack to implement setPixels(java.lang.Object, int).
    Set all pixels in the specified XY-plane.
    
    Parameters:
    
    index - Zero based index of the plane. (Warning VirtualStack.getPixels(int) uses one base indices).
    
    pixels - Array that contains the pixel data. Array length must equal getWidth() times getHeight(). Type of the array must be byte[], short[], int[] or float[] and match the type indicated by getBitDepth().
  - getSliceZeroBasedIndex
```
protected RandomAccessibleInterval<?> getSliceZeroBasedIndex(int index)
```
    This method is used internally by AbstractVirtualStack to implement getVoxels(int, int, int, int, int, int, float[]) and setVoxels(int, int, int, int, int, int, float[]).
    Returns a two dimensional RandomAccessibleInterval that provides read and write access to the specified XY-plane. The pixel type must be match getBitDepth(). RealType for 8, 16 and 32 bit images, and ARGBType fot 32-bit images.
    
    Parameters:
    
    index - Zero based index of the plane. (Warning VirtualStack.getPixels(int) uses one base indices).
  - getProcessor
```
public ij.process.ImageProcessor getProcessor(int n)
```
    Overrides:
    
    getProcessor in class ij.VirtualStack
  - addSlice
```
public void addSlice(String name)
```
    Overrides:
    
    addSlice in class ij.VirtualStack
  - addSlice
```
public void addSlice(String sliceLabel,
                     Object pixels)
```
    Overrides:
    
    addSlice in class ij.VirtualStack
  - addSlice
```
public void addSlice(String sliceLabel,
                     ij.process.ImageProcessor ip)
```
    Overrides:
    
    addSlice in class ij.VirtualStack
  - addSlice
```
public void addSlice(String sliceLabel,
                     ij.process.ImageProcessor ip,
                     int n)
```
    Overrides:
    
    addSlice in class ij.VirtualStack
  - deleteSlice
```
public void deleteSlice(int n)
```
    Overrides:
    
    deleteSlice in class ij.VirtualStack
  - deleteLastSlice
```
public void deleteLastSlice()
```
    Overrides:
    
    deleteLastSlice in class ij.VirtualStack
  - saveChanges
```
public int saveChanges(int n)
```
    Currently not implemented
    
    Overrides:
    
    saveChanges in class ij.VirtualStack
  - getSize
```
public int getSize()
```
    Overrides:
    
    getSize in class ij.VirtualStack
  - getSliceLabel
```
public String getSliceLabel(int n)
```
    Overrides:
    
    getSliceLabel in class ij.VirtualStack
  - getImageArray
```
public Object[] getImageArray()
```
    Overrides:
    
    getImageArray in class ij.VirtualStack
  - setSliceLabel
```
public void setSliceLabel(String label,
                          int n)
```
    Overrides:
    
    setSliceLabel in class ij.VirtualStack
  - isVirtual
```
public boolean isVirtual()
```
    Overrides:
    
    isVirtual in class ij.VirtualStack
  - trim
```
public void trim()
```
    Overrides:
    
    trim 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
  - setBitDepth
```
public void setBitDepth(int bitDepth)
```
    Overrides:
    
    setBitDepth in class ij.VirtualStack
  - getBitDepth
```
public int getBitDepth()
```
    Overrides:
    
    getBitDepth in class ij.VirtualStack
  - sortDicom
```
public ij.ImageStack sortDicom(String[] strings,
                               String[] info,
                               int maxDigits)
```
    Overrides:
    
    sortDicom in class ij.VirtualStack
  - addUnsignedShortSlice
```
public void addUnsignedShortSlice(String sliceLabel,
                                  Object pixels)
```
    Overrides:
    
    addUnsignedShortSlice in class ij.ImageStack
  - addSlice
```
public void addSlice(ij.process.ImageProcessor ip)
```
    Overrides:
    
    addSlice in class ij.ImageStack
  - getWidth
```
public int getWidth()
```
    Overrides:
    
    getWidth in class ij.ImageStack
  - getHeight
```
public int getHeight()
```
    Overrides:
    
    getHeight in class ij.ImageStack
  - setRoi
```
public void setRoi(Rectangle roi)
```
    Overrides:
    
    setRoi in class ij.ImageStack
  - getRoi
```
public Rectangle getRoi()
```
    Overrides:
    
    getRoi in class ij.ImageStack
  - update
```
public void update(ij.process.ImageProcessor ip)
```
    Overrides:
    
    update in class ij.ImageStack
  - size
```
public int size()
```
    Overrides:
    
    size in class ij.VirtualStack
  - getSliceLabels
```
public String[] getSliceLabels()
```
    Overrides:
    
    getSliceLabels in class ij.ImageStack
  - getShortSliceLabel
```
public String getShortSliceLabel(int n)
```
    Overrides:
    
    getShortSliceLabel in class ij.ImageStack
  - setProcessor
```
public void setProcessor(ij.process.ImageProcessor ip,
                         int n)
```
    Overrides:
    
    setProcessor in class ij.ImageStack
  - setColorModel
```
public void setColorModel(ColorModel cm)
```
    Overrides:
    
    setColorModel in class ij.ImageStack
  - getColorModel
```
public ColorModel getColorModel()
```
    Overrides:
    
    getColorModel in class ij.ImageStack
  - isRGB
```
public boolean isRGB()
```
    Overrides:
    
    isRGB in class ij.ImageStack
  - isHSB
```
public boolean isHSB()
```
    Overrides:
    
    isHSB in class ij.ImageStack
  - isLab
```
public boolean isLab()
```
    Overrides:
    
    isLab in class ij.ImageStack
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class ij.ImageStack
  - getVoxels
```
public float[] getVoxels(int x0,
                         int y0,
                         int z0,
                         int w,
                         int h,
                         int d,
                         float[] voxels)
```
    Overrides:
    
    getVoxels in class ij.ImageStack
  - getVoxels
```
public float[] getVoxels(int x0,
                         int y0,
                         int z0,
                         int w,
                         int h,
                         int d,
                         float[] voxels,
                         int channel)
```
    Overrides:
    
    getVoxels in class ij.ImageStack
  - setVoxels
```
public void setVoxels(int x0,
                      int y0,
                      int z0,
                      int w,
                      int h,
                      int d,
                      float[] voxels)
```
    Overrides:
    
    setVoxels in class ij.ImageStack
  - setVoxels
```
public void setVoxels(int x0,
                      int y0,
                      int z0,
                      int w,
                      int h,
                      int d,
                      float[] voxels,
                      int channel)
```
    Overrides:
    
    setVoxels in class ij.ImageStack
  - drawSphere
```
public void drawSphere(double radius,
                       int xc,
                       int yc,
                       int zc)
```
    Overrides:
    
    drawSphere in class ij.ImageStack
  - duplicate
```
public ij.ImageStack duplicate()
```
    Overrides:
    
    duplicate in class ij.ImageStack
  - crop
```
public ij.ImageStack crop(int x,
                          int y,
                          int z,
                          int width,
                          int height,
                          int depth)
```
    Overrides:
    
    crop in class ij.ImageStack
  - convertToFloat
```
public ij.ImageStack convertToFloat()
```
    Overrides:
    
    convertToFloat in class ij.ImageStack

Class AbstractVirtualStack

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

AbstractVirtualStack

Method Detail

setMinAndMax

getPixels

setPixels

isWritable

getPixelsZeroBasedIndex

setPixelsZeroBasedIndex

getSliceZeroBasedIndex

getProcessor

addSlice

addSlice

addSlice

addSlice

deleteSlice

deleteLastSlice

saveChanges

getSize

getSliceLabel

getImageArray

setSliceLabel

isVirtual

trim

getDirectory

getFileName

setBitDepth

getBitDepth

sortDicom

addUnsignedShortSlice

addSlice

getWidth

getHeight

setRoi

getRoi

update

size

getSliceLabels

getShortSliceLabel

setProcessor

setColorModel

getColorModel

isRGB

isHSB

isLab

toString

getVoxels

getVoxels

setVoxels

setVoxels

drawSphere

duplicate

crop

convertToFloat