StackLink (LOCI Javadocs 0-SNAPSHOT API)

java.lang.Object
- loci.visbio.view.TransformLink
- - loci.visbio.view.StackLink

All Implemented Interfaces:

Runnable, EventListener, TransformListener, Dynamic, Saveable, DisplayListener
```
public class StackLink
extends TransformLink
```
Represents a link between a data transform and a display that produces an image stack.

Field Summary

Fields
Modifier and Type	Field and Description
`protected boolean`	`axisValid` Flag indicating whether stackAxis is valid.
`protected int`	`currentSlice` Data transform's current slice.
`protected static Data`	`DUMMY` Dummy data to avoid "Data is null" message for volume reference.
`protected int[]`	`lastPos` Last known dimensional position of the link.
`protected Vector<DataReference>`	`references` Data references linking data to the display.
`protected Vector<DataRenderer>`	`renderers` Data renderers for toggling data's visibility and other parameters.
`protected int`	`stackAxis` Dimensional axis to use for image stacks.
`protected boolean[]`	`visSlices` Flags indicating visibility of each slice of the stack.
`protected boolean`	`volume` Whether volume rendering is currently enabled.
`protected DataReferenceImpl`	`volumeRef` Data reference for volume rendered cube.
`protected int`	`volumeRes` Resolution of rendered volumes.

Fields inherited from class loci.visbio.view.TransformLink
alive, burnNow, burnThread, burnTime, cachedPos, clearWhenDone, colorHandler, cursor, handler, ref, rend, status, trans, visible

Constructor Summary

Constructors
Constructor and Description
`StackLink(StackHandler h)` Constructs an uninitialized stack link.
`StackLink(StackHandler h, DataTransform t)` Creates a link between the given data transform and the specified stack handler's display.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected void`	`computeCursor()` Computes range values at the current cursor location.
`protected void`	`computeData(boolean thumbs)` Computes the reference data at the current position, utilizing thumbnails as appropriate.
`protected void`	`doTransform()` Updates the currently displayed data for the given transform.
`int`	`getCurrentSlice()` Gets the current slice index, assuming the currently assigned stack axis.
`protected Data`	`getImageData(int[] pos)` Gets 2D data from the specified data transform.
`DataReferenceImpl[]`	`getReferences()` Gets references corresponding to each plane in the image stack.
`DataRenderer[]`	`getRenderers()` Gets renderers corresponding to each plane in the image stack.
`int`	`getSliceCount()` Gets the number of slices, assuming the currently assigned stack axis.
`int`	`getStackAxis()` Gets the currently assigned stack axis.
`int`	`getVolumeResolution()` Gets maximum resolution per axis of rendered volumes.
`void`	`initState(Dynamic dyn)` Modifies this object's state to match that of the given object.
`boolean`	`isBoundingBoxVisible()` Gets visibility of the given data transform's yellow bounding box.
`boolean`	`isCompatible(Dynamic dyn)` Tests whether the given dynamic object can be used as an argument to initState, for initializing this dynamic object.
`boolean`	`isSliceVisible(int slice)` Gets visibility at the specified slice index.
`boolean`	`isVisible()` Gets visibility of the transform.
`boolean`	`isVolumeRendered()` Gets status of volume rendering.
`void`	`link()` Links this stack into the display.
`boolean`	`matches(Dynamic dyn)` Tests whether two dynamic objects are equivalent.
`void`	`restoreState(Element el)` Restores the current state from the given DOM element ("StackLink").
`void`	`saveState(Element el)` Writes the current state to the given DOM element ("LinkedData").
`void`	`setBoundingBoxVisible(boolean vis)` Enables or disables visibility of the yellow bounding box.
`protected void`	`setData(Data d, DataReference dataRef, DataRenderer dataRend, boolean autoSwitch, double zval)` Assigns the given data object to the specified data reference, switching to the proper types if the flag is set.
`void`	`setSliceVisible(int slice, boolean vis)` Enables or disables visibility at the specified slice index.
`void`	`setStackAxis(int axis)` Assigns the given axis as the stack axis.
`void`	`setVisible(boolean vis)` Toggles visibility of the transform.
`void`	`setVolumeRendered(boolean volume)` Enables or disables volume rendering.
`void`	`setVolumeResolution(int res)` Sets maximum resolution per axis of rendered volumes.
`protected void`	`setZLevel(DataRenderer rend, double zval, int len)` Assigns the given value to the specified data renderer's ConstantMap to the Z axis.
`void`	`unlink()` Unlinks this stack from the display.

Methods inherited from class loci.visbio.view.TransformLink
destroy, discard, displayChanged, doTransform, doTransform, getColorHandler, getHandler, getReference, getRenderer, getTransform, run, setData, setData, setData, setData, setMessage, transformChanged

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

- Field Detail
  - DUMMY
```
protected static final Data DUMMY
```
    Dummy data to avoid "Data is null" message for volume reference.
  - references
```
protected Vector<DataReference> references
```
    Data references linking data to the display.
  - renderers
```
protected Vector<DataRenderer> renderers
```
    Data renderers for toggling data's visibility and other parameters.
  - stackAxis
```
protected int stackAxis
```
    Dimensional axis to use for image stacks.
  - axisValid
```
protected boolean axisValid
```
    Flag indicating whether stackAxis is valid. If it is not, it will be autodetected when initState is called. Also, if it is valid, then setStackAxis will not rebuild display references unless the new axis value is different from the old one.
  - lastPos
```
protected int[] lastPos
```
    Last known dimensional position of the link.
  - volumeRef
```
protected DataReferenceImpl volumeRef
```
    Data reference for volume rendered cube.
  - volume
```
protected boolean volume
```
    Whether volume rendering is currently enabled.
  - volumeRes
```
protected int volumeRes
```
    Resolution of rendered volumes.
  - currentSlice
```
protected int currentSlice
```
    Data transform's current slice.
  - visSlices
```
protected boolean[] visSlices
```
    Flags indicating visibility of each slice of the stack. Used for both initial state and temporary storage while volume rendering.
- Constructor Detail
  - StackLink
```
public StackLink(StackHandler h)
```
    Constructs an uninitialized stack link.
  - StackLink
```
public StackLink(StackHandler h,
                 DataTransform t)
```
    Creates a link between the given data transform and the specified stack handler's display.
- Method Detail
  - getReferences
```
public DataReferenceImpl[] getReferences()
```
    Gets references corresponding to each plane in the image stack.
  - getRenderers
```
public DataRenderer[] getRenderers()
```
    Gets renderers corresponding to each plane in the image stack.
  - setStackAxis
```
public void setStackAxis(int axis)
```
    Assigns the given axis as the stack axis.
  - getStackAxis
```
public int getStackAxis()
```
    Gets the currently assigned stack axis.
  - getSliceCount
```
public int getSliceCount()
```
    Gets the number of slices, assuming the currently assigned stack axis.
  - getCurrentSlice
```
public int getCurrentSlice()
```
    Gets the current slice index, assuming the currently assigned stack axis.
  - setSliceVisible
```
public void setSliceVisible(int slice,
                            boolean vis)
```
    Enables or disables visibility at the specified slice index.
  - isSliceVisible
```
public boolean isSliceVisible(int slice)
```
    Gets visibility at the specified slice index.
  - setBoundingBoxVisible
```
public void setBoundingBoxVisible(boolean vis)
```
    Enables or disables visibility of the yellow bounding box.
  - isBoundingBoxVisible
```
public boolean isBoundingBoxVisible()
```
    Gets visibility of the given data transform's yellow bounding box.
  - setVolumeRendered
```
public void setVolumeRendered(boolean volume)
```
    Enables or disables volume rendering.
  - isVolumeRendered
```
public boolean isVolumeRendered()
```
    Gets status of volume rendering.
  - setVolumeResolution
```
public void setVolumeResolution(int res)
```
    Sets maximum resolution per axis of rendered volumes.
  - getVolumeResolution
```
public int getVolumeResolution()
```
    Gets maximum resolution per axis of rendered volumes.
  - link
```
public void link()
```
    Links this stack into the display.
    
    Overrides:
    
    link in class TransformLink
  - unlink
```
public void unlink()
```
    Unlinks this stack from the display.
    
    Overrides:
    
    unlink in class TransformLink
  - setVisible
```
public void setVisible(boolean vis)
```
    Toggles visibility of the transform.
    
    Overrides:
    
    setVisible in class TransformLink
  - isVisible
```
public boolean isVisible()
```
    Gets visibility of the transform.
    
    Overrides:
    
    isVisible in class TransformLink
  - matches
```
public boolean matches(Dynamic dyn)
```
    Tests whether two dynamic objects are equivalent.
    
    Specified by:
    
    matches in interface Dynamic
    
    Overrides:
    
    matches in class TransformLink
  - isCompatible
```
public boolean isCompatible(Dynamic dyn)
```
    Tests whether the given dynamic object can be used as an argument to initState, for initializing this dynamic object.
    
    Specified by:
    
    isCompatible in interface Dynamic
    
    Overrides:
    
    isCompatible in class TransformLink
  - initState
```
public void initState(Dynamic dyn)
```
    Modifies this object's state to match that of the given object. If the argument is null, the object is initialized according to its current state instead.
    
    Specified by:
    
    initState in interface Dynamic
    
    Overrides:
    
    initState in class TransformLink
  - saveState
```
public void saveState(Element el)
               throws SaveException
```
    Writes the current state to the given DOM element ("LinkedData").
    
    Specified by:
    
    saveState in interface Saveable
    
    Overrides:
    
    saveState in class TransformLink
    
    Throws:
    
    SaveException
  - restoreState
```
public void restoreState(Element el)
                  throws SaveException
```
    Restores the current state from the given DOM element ("StackLink").
    
    Specified by:
    
    restoreState in interface Saveable
    
    Overrides:
    
    restoreState in class TransformLink
    
    Throws:
    
    SaveException
  - setData
```
protected void setData(Data d,
                       DataReference dataRef,
                       DataRenderer dataRend,
                       boolean autoSwitch,
                       double zval)
```
    Assigns the given data object to the specified data reference, switching to the proper types if the flag is set.
  - setZLevel
```
protected void setZLevel(DataRenderer rend,
                         double zval,
                         int len)
```
    Assigns the given value to the specified data renderer's ConstantMap to the Z axis.
  - doTransform
```
protected void doTransform()
```
    Updates the currently displayed data for the given transform.
    
    Overrides:
    
    doTransform in class TransformLink
  - computeData
```
protected void computeData(boolean thumbs)
```
    Computes the reference data at the current position, utilizing thumbnails as appropriate.
    
    Overrides:
    
    computeData in class TransformLink
  - getImageData
```
protected Data getImageData(int[] pos)
```
    Gets 2D data from the specified data transform.
    
    Overrides:
    
    getImageData in class TransformLink
  - computeCursor
```
protected void computeCursor()
```
    Computes range values at the current cursor location.
    
    Overrides:
    
    computeCursor in class TransformLink

Class StackLink

Field Summary

Fields inherited from class loci.visbio.view.TransformLink

Constructor Summary

Method Summary

Methods inherited from class loci.visbio.view.TransformLink

Methods inherited from class java.lang.Object

Field Detail

DUMMY

references

renderers

stackAxis

axisValid

lastPos

volumeRef

volume

volumeRes

currentSlice

visSlices

Constructor Detail

StackLink

StackLink

Method Detail

getReferences

getRenderers

setStackAxis

getStackAxis

getSliceCount

getCurrentSlice

setSliceVisible

isSliceVisible

setBoundingBoxVisible

isBoundingBoxVisible

setVolumeRendered

isVolumeRendered

setVolumeResolution

getVolumeResolution

link

unlink

setVisible

isVisible

matches

isCompatible

initState

saveState

restoreState

setData

setZLevel

doTransform

computeData

getImageData

computeCursor